TODO in the future:

KEGG functions

GO functions

 

Protein Aggregation

Proteasome


KEGG

proteasome_pathway_id = 'hsa03050'
proteasome_brite_id = 'ko03051'
Image(REST.kegg_get(proteasome_pathway_id, 'image').read())
proteasome_pathway_genes = get_KEGG_pathway_gene_members(proteasome_pathway_id)
proteasome_brite_genes = get_KEGG_BRITE_entry(proteasome_brite_id)
proteasome_brite_genes = proteasome_brite_genes.loc['Eukaryotic proteasome']
proteasome_brite_genes['in_KEGG_pathway'] = proteasome_brite_genes.ENSG.isin(proteasome_pathway_genes.ENSG).astype(int)
proteasome_brite_genes.to_pickle('targets/proteasome_brite.pickle')

GO

proteasome_subgraph, proteasome_nodes = GO_subgraph_from_query('proteasom')
draw_graph(proteasome_subgraph)
negative regulation of SCF-dependent proteasomal ubiquitin-dependent catabolic process negative regulation of SCF-dependent proteasomal ubiquitin-dependent catabolic process regulation of SCF-dependent proteasomal ubiquitin-dependent protein catabolic process regulation of SCF-dependent proteasomal ubiquitin-dependent protein catabolic process negative regulation of SCF-dependent proteasomal ubiquitin-dependent catabolic process->regulation of SCF-dependent proteasomal ubiquitin-dependent protein catabolic process negative regulation of proteasomal ubiquitin-dependent protein catabolic process negative regulation of proteasomal ubiquitin-dependent protein catabolic process negative regulation of SCF-dependent proteasomal ubiquitin-dependent catabolic process->negative regulation of proteasomal ubiquitin-dependent protein catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process regulation of SCF-dependent proteasomal ubiquitin-dependent protein catabolic process->regulation of proteasomal ubiquitin-dependent protein catabolic process negative regulation of proteasomal ubiquitin-dependent protein catabolic process->regulation of proteasomal ubiquitin-dependent protein catabolic process negative regulation of proteasomal protein catabolic process negative regulation of proteasomal protein catabolic process negative regulation of proteasomal ubiquitin-dependent protein catabolic process->negative regulation of proteasomal protein catabolic process positive regulation of proteasomal protein catabolic process positive regulation of proteasomal protein catabolic process regulation of proteasomal protein catabolic process regulation of proteasomal protein catabolic process positive regulation of proteasomal protein catabolic process->regulation of proteasomal protein catabolic process protein localization to cytosolic proteasome complex involved in ERAD pathway protein localization to cytosolic proteasome complex involved in ERAD pathway protein localization to cytosolic proteasome complex protein localization to cytosolic proteasome complex protein localization to cytosolic proteasome complex involved in ERAD pathway->protein localization to cytosolic proteasome complex proteasome accessory complex proteasome accessory complex proteasome complex proteasome complex proteasome accessory complex->proteasome complex cytosolic proteasome regulatory particle cytosolic proteasome regulatory particle cytosolic proteasome complex cytosolic proteasome complex cytosolic proteasome regulatory particle->cytosolic proteasome complex proteasome regulatory particle proteasome regulatory particle cytosolic proteasome regulatory particle->proteasome regulatory particle cytosolic proteasome complex->proteasome complex proteasome regulatory particle->proteasome accessory complex nuclear proteasome regulatory particle nuclear proteasome regulatory particle nuclear proteasome regulatory particle->proteasome regulatory particle nuclear proteasome complex nuclear proteasome complex nuclear proteasome regulatory particle->nuclear proteasome complex nuclear proteasome complex->proteasome complex protein polyubiquitination involved in nucleus-associated proteasomal ubiquitin-dependent protein catabolic process protein polyubiquitination involved in nucleus-associated proteasomal ubiquitin-dependent protein catabolic process nuclear protein quality control by the ubiquitin-proteasome system nuclear protein quality control by the ubiquitin-proteasome system protein polyubiquitination involved in nucleus-associated proteasomal ubiquitin-dependent protein catabolic process->nuclear protein quality control by the ubiquitin-proteasome system proteasome-mediated ubiquitin-dependent protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process nuclear protein quality control by the ubiquitin-proteasome system->proteasome-mediated ubiquitin-dependent protein catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process->regulation of proteasomal protein catabolic process proteasomal ubiquitin-independent protein catabolic process proteasomal ubiquitin-independent protein catabolic process proteasomal protein catabolic process proteasomal protein catabolic process proteasomal ubiquitin-independent protein catabolic process->proteasomal protein catabolic process cytosolic proteasome core complex cytosolic proteasome core complex cytosolic proteasome core complex->cytosolic proteasome complex proteasome core complex proteasome core complex cytosolic proteasome core complex->proteasome core complex proteasome core complex->proteasome complex nuclear proteasome core complex, alpha-subunit complex nuclear proteasome core complex, alpha-subunit complex nuclear proteasome core complex nuclear proteasome core complex nuclear proteasome core complex, alpha-subunit complex->nuclear proteasome core complex proteasome core complex, alpha-subunit complex proteasome core complex, alpha-subunit complex nuclear proteasome core complex, alpha-subunit complex->proteasome core complex, alpha-subunit complex nuclear proteasome core complex->nuclear proteasome complex nuclear proteasome core complex->proteasome core complex proteasome core complex, alpha-subunit complex->proteasome core complex nuclear proteasome regulatory particle, base subcomplex nuclear proteasome regulatory particle, base subcomplex nuclear proteasome regulatory particle, base subcomplex->nuclear proteasome regulatory particle proteasome regulatory particle, base subcomplex proteasome regulatory particle, base subcomplex nuclear proteasome regulatory particle, base subcomplex->proteasome regulatory particle, base subcomplex proteasome regulatory particle, base subcomplex->proteasome regulatory particle positive regulation of SCF-dependent proteasomal ubiquitin-dependent catabolic process positive regulation of SCF-dependent proteasomal ubiquitin-dependent catabolic process positive regulation of SCF-dependent proteasomal ubiquitin-dependent catabolic process->regulation of SCF-dependent proteasomal ubiquitin-dependent protein catabolic process positive regulation of proteasomal ubiquitin-dependent protein catabolic process positive regulation of proteasomal ubiquitin-dependent protein catabolic process positive regulation of SCF-dependent proteasomal ubiquitin-dependent catabolic process->positive regulation of proteasomal ubiquitin-dependent protein catabolic process positive regulation of proteasomal ubiquitin-dependent protein catabolic process->positive regulation of proteasomal protein catabolic process positive regulation of proteasomal ubiquitin-dependent protein catabolic process->regulation of proteasomal ubiquitin-dependent protein catabolic process SCF-dependent proteasomal ubiquitin-dependent protein catabolic process SCF-dependent proteasomal ubiquitin-dependent protein catabolic process SCF-dependent proteasomal ubiquitin-dependent protein catabolic process->proteasome-mediated ubiquitin-dependent protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process->proteasomal protein catabolic process nuclear proteasome regulatory particle, lid subcomplex nuclear proteasome regulatory particle, lid subcomplex nuclear proteasome regulatory particle, lid subcomplex->nuclear proteasome regulatory particle proteasome regulatory particle, lid subcomplex proteasome regulatory particle, lid subcomplex nuclear proteasome regulatory particle, lid subcomplex->proteasome regulatory particle, lid subcomplex proteasome regulatory particle, lid subcomplex->proteasome regulatory particle proteasome complex disassembly proteasome complex disassembly proteasome storage granule assembly proteasome storage granule assembly proteasome-activating nucleotidase complex proteasome-activating nucleotidase complex proteasome-activating nucleotidase complex->proteasome accessory complex cytosolic proteasome core complex, alpha-subunit complex cytosolic proteasome core complex, alpha-subunit complex cytosolic proteasome core complex, alpha-subunit complex->cytosolic proteasome core complex cytosolic proteasome core complex, alpha-subunit complex->proteasome core complex, alpha-subunit complex proteasome storage granule proteasome storage granule proteasome assembly proteasome assembly regulation of proteasome assembly regulation of proteasome assembly cytoplasm protein quality control by the ubiquitin-proteasome system cytoplasm protein quality control by the ubiquitin-proteasome system cytoplasm protein quality control by the ubiquitin-proteasome system->proteasome-mediated ubiquitin-dependent protein catabolic process proteasome storage granule disassembly proteasome storage granule disassembly negative regulation of proteasomal protein catabolic process->regulation of proteasomal protein catabolic process regulation of proteasome core complex assembly regulation of proteasome core complex assembly regulation of proteasome core complex assembly->regulation of proteasome assembly proteasome-nuclear membrane anchor activity proteasome-nuclear membrane anchor activity proteasome core complex, beta-subunit complex proteasome core complex, beta-subunit complex proteasome core complex, beta-subunit complex->proteasome core complex nuclear proteasome core complex, beta-subunit complex nuclear proteasome core complex, beta-subunit complex nuclear proteasome core complex, beta-subunit complex->nuclear proteasome core complex nuclear proteasome core complex, beta-subunit complex->proteasome core complex, beta-subunit complex proteasome core complex binding proteasome core complex binding spermatoproteasome complex spermatoproteasome complex spermatoproteasome complex->proteasome complex proteasome core complex import into nucleus proteasome core complex import into nucleus cytosolic proteasome regulatory particle, base subcomplex cytosolic proteasome regulatory particle, base subcomplex cytosolic proteasome regulatory particle, base subcomplex->cytosolic proteasome regulatory particle cytosolic proteasome regulatory particle, base subcomplex->proteasome regulatory particle, base subcomplex proteasome binding proteasome binding proteasome localization to nuclear periphery proteasome localization to nuclear periphery proteasome localization proteasome localization proteasome localization to nuclear periphery->proteasome localization cytosolic proteasome regulatory particle, lid subcomplex cytosolic proteasome regulatory particle, lid subcomplex cytosolic proteasome regulatory particle, lid subcomplex->cytosolic proteasome regulatory particle cytosolic proteasome regulatory particle, lid subcomplex->proteasome regulatory particle, lid subcomplex positive regulation of proteasomal ubiquitin-dependent protein catabolic process involved in cellular response to hypoxia positive regulation of proteasomal ubiquitin-dependent protein catabolic process involved in cellular response to hypoxia positive regulation of proteasomal ubiquitin-dependent protein catabolic process involved in cellular response to hypoxia->positive regulation of proteasomal ubiquitin-dependent protein catabolic process proteasome activator complex proteasome activator complex proteasome activator complex->proteasome accessory complex proteasome-activating activity proteasome-activating activity proteasome regulatory particle binding proteasome regulatory particle binding cytosolic proteasome core complex, beta-subunit complex cytosolic proteasome core complex, beta-subunit complex cytosolic proteasome core complex, beta-subunit complex->cytosolic proteasome core complex cytosolic proteasome core complex, beta-subunit complex->proteasome core complex, beta-subunit complex proteasome regulatory particle assembly proteasome regulatory particle assembly proteasome regulatory particle assembly->proteasome assembly proteasomal proteolysis associated with antigen processing and presentation proteasomal proteolysis associated with antigen processing and presentation proteasome core complex assembly proteasome core complex assembly proteasome core complex assembly->proteasome assembly structural constituent of proteasome structural constituent of proteasome
df = create_GO_by_gene_matrix(proteasome_nodes, attr='gene_name')
df = sort_df_by_hclust_olo(df)
ax = plot_gene_membership_in_GO_terms(df, figsize=(6, 10))
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd"> 2022-08-01T19:44:39.117055 image/svg+xml Matplotlib v3.5.2, https://matplotlib.org/
proteasome_nodes.to_pickle('targets/proteasome_GO.pickle')

Overlap

KEGG_GO_venn(proteasome_brite_genes, proteasome_nodes)
<matplotlib_venn._common.VennDiagram at 0x1a9bc0fa0>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd"> 2022-08-01T19:44:40.435437 image/svg+xml Matplotlib v3.5.2, https://matplotlib.org/

Chaperones


KEGG

chaperones_brite_id = 'ko03110'
chaperones_brite_genes = get_KEGG_BRITE_entry(chaperones_brite_id)
chaperones_brite_genes.to_pickle('targets/chaperone_brite.pickle')

GO

chaperone_subgraph, chaperone_nodes = GO_subgraph_from_query('chaperone')
draw_graph(chaperone_subgraph)
df = create_GO_by_gene_matrix(chaperone_nodes, attr='gene_name')
df = sort_df_by_hclust_olo(df)
ax = plot_gene_membership_in_GO_terms(df, figsize=(6, 10))
histone chaperone activity histone chaperone activity protein carrier chaperone protein carrier chaperone histone chaperone activity->protein carrier chaperone chaperone-mediated autophagy translocation complex disassembly chaperone-mediated autophagy translocation complex disassembly chaperone-mediated autophagy translocation complex chaperone-mediated autophagy translocation complex ATP-dependent H3-H4 histone complex chaperone activity ATP-dependent H3-H4 histone complex chaperone activity ATP-dependent histone chaperone activity ATP-dependent histone chaperone activity ATP-dependent H3-H4 histone complex chaperone activity->ATP-dependent histone chaperone activity H3-H4 histone complex chaperone activity H3-H4 histone complex chaperone activity ATP-dependent H3-H4 histone complex chaperone activity->H3-H4 histone complex chaperone activity ATP-dependent histone chaperone activity->histone chaperone activity H3-H4 histone complex chaperone activity->histone chaperone activity regulation of chaperone-mediated protein complex assembly regulation of chaperone-mediated protein complex assembly metallochaperone activity metallochaperone activity chaperone binding chaperone binding superoxide dismutase copper chaperone activity superoxide dismutase copper chaperone activity copper chaperone activity copper chaperone activity superoxide dismutase copper chaperone activity->copper chaperone activity copper chaperone activity->metallochaperone activity zinc chaperone activity zinc chaperone activity zinc chaperone activity->metallochaperone activity regulation of chaperone-mediated protein folding regulation of chaperone-mediated protein folding regulation of chaperone-mediated autophagy regulation of chaperone-mediated autophagy protein targeting to lysosome involved in chaperone-mediated autophagy protein targeting to lysosome involved in chaperone-mediated autophagy chaperone-mediated autophagy chaperone-mediated autophagy protein targeting to lysosome involved in chaperone-mediated autophagy->chaperone-mediated autophagy ATP-dependent FeS chaperone activity ATP-dependent FeS chaperone activity ATP-dependent FeS chaperone activity->metallochaperone activity iron chaperone activity iron chaperone activity iron chaperone activity->metallochaperone activity chaperone complex chaperone complex ATP-dependent protein folding chaperone ATP-dependent protein folding chaperone protein folding chaperone protein folding chaperone ATP-dependent protein folding chaperone->protein folding chaperone vacuolar transporter chaperone complex vacuolar transporter chaperone complex vacuolar transporter chaperone complex->chaperone complex chaperone mediated protein folding independent of cofactor chaperone mediated protein folding independent of cofactor chaperone-mediated protein folding chaperone-mediated protein folding chaperone mediated protein folding independent of cofactor->chaperone-mediated protein folding positive regulation of chaperone-mediated autophagy positive regulation of chaperone-mediated autophagy positive regulation of chaperone-mediated autophagy->regulation of chaperone-mediated autophagy chaperone-mediated protein complex assembly chaperone-mediated protein complex assembly ATP-dependent H2AZ histone chaperone activity ATP-dependent H2AZ histone chaperone activity ATP-dependent H2AZ histone chaperone activity->ATP-dependent histone chaperone activity RNA folding chaperone RNA folding chaperone HSP90-CDC37 chaperone complex HSP90-CDC37 chaperone complex HSP90-CDC37 chaperone complex->chaperone complex chaperone-mediated autophagy translocation complex assembly chaperone-mediated autophagy translocation complex assembly chaperone-mediated autophagy translocation complex assembly->chaperone-mediated autophagy chaperone cofactor-dependent protein refolding chaperone cofactor-dependent protein refolding chaperone cofactor-dependent protein refolding->chaperone-mediated protein folding endoplasmic reticulum chaperone complex endoplasmic reticulum chaperone complex positive regulation of chaperone-mediated protein complex assembly positive regulation of chaperone-mediated protein complex assembly positive regulation of chaperone-mediated protein complex assembly->regulation of chaperone-mediated protein complex assembly metallochaperone complex metallochaperone complex negative regulation of chaperone-mediated protein folding negative regulation of chaperone-mediated protein folding negative regulation of chaperone-mediated protein folding->regulation of chaperone-mediated protein folding positive regulation of chaperone-mediated protein folding positive regulation of chaperone-mediated protein folding positive regulation of chaperone-mediated protein folding->regulation of chaperone-mediated protein folding H2A-H2B histone complex chaperone activity H2A-H2B histone complex chaperone activity H2A-H2B histone complex chaperone activity->histone chaperone activity negative regulation of chaperone-mediated autophagy negative regulation of chaperone-mediated autophagy negative regulation of chaperone-mediated autophagy->regulation of chaperone-mediated autophagy Ig heavy chain-bound endoplasmic reticulum chaperone complex Ig heavy chain-bound endoplasmic reticulum chaperone complex Ig heavy chain-bound endoplasmic reticulum chaperone complex->chaperone complex superoxide dismutase copper chaperone complex superoxide dismutase copper chaperone complex superoxide dismutase copper chaperone complex->metallochaperone complex
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd"> 2022-08-01T19:44:42.431906 image/svg+xml Matplotlib v3.5.2, https://matplotlib.org/
chaperone_nodes.to_pickle('targets/chaperone_GO.pickle')

Overlap

KEGG_GO_venn(chaperones_brite_genes, chaperone_nodes)
<matplotlib_venn._common.VennDiagram at 0x1a9cdd940>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd"> 2022-08-01T19:44:43.002047 image/svg+xml Matplotlib v3.5.2, https://matplotlib.org/

Autophagy


KEGG

autophagy_KEGG_pathway = 'hsa04140'
autophagy_KEGG_BRITE = 'ko04131'
Image(REST.kegg_get(autophagy_KEGG_pathway, 'image').read())
autophagy_pathway_genes = get_KEGG_pathway_gene_members(autophagy_KEGG_pathway)
autophagy_brite_genes = get_KEGG_BRITE_entry(autophagy_KEGG_BRITE)
autophagy_brite_genes = autophagy_brite_genes.loc['Autophagy']
autophagy_brite_genes['in_KEGG_pathway'] = autophagy_brite_genes.ENSG.isin(autophagy_pathway_genes.ENSG).astype(int)
autophagy_brite_genes.to_pickle('targets/autophagy_brite.pickle')

GO

autophagy_subgraph, autophagy_nodes = GO_subgraph_from_query('autophag')
df = create_GO_by_gene_matrix(autophagy_nodes, attr='gene_name')
df = sort_df_by_hclust_olo(df)
clustermap = plot_gene_membership_in_GO_terms(df, figsize=(6, 10))
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd"> 2022-08-01T19:44:52.029688 image/svg+xml Matplotlib v3.5.2, https://matplotlib.org/
autophagy_nodes.to_pickle('targets/autophagy_GO.pickle')

Overlap

KEGG_GO_venn(autophagy_brite_genes, autophagy_nodes)
<matplotlib_venn._common.VennDiagram at 0x19a056520>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd"> 2022-08-01T19:44:54.058061 image/svg+xml Matplotlib v3.5.2, https://matplotlib.org/

Mitophagy


KEGG

mitophagy_KEGG_pathway = 'hsa04137'
Image(REST.kegg_get(mitophagy_KEGG_pathway, 'image').read())
mitophagy_pathway_genes = get_KEGG_pathway_gene_members(mitophagy_KEGG_pathway)
mitophagy_brite_genes = pd.DataFrame(autophagy_brite_genes.loc['Mitophagy'])
mitophagy_brite_genes.drop(['in_KEGG_pathway'], axis=1, inplace=True)
mitophagy_brite_genes['in_KEGG_pathway'] = mitophagy_brite_genes.ENSG.isin(mitophagy_pathway_genes.ENSG).astype(int)
mitophagy_brite_genes.to_pickle('targets/mitophagy_brite.pickle')

GO

mitophagy_subgraph, mitophagy_nodes = GO_subgraph_from_query('mitophagy')
df = create_GO_by_gene_matrix(mitophagy_nodes, attr='gene_name')
df = sort_df_by_hclust_olo(df)
ax = plot_gene_membership_in_GO_terms(df, figsize=(6, 10))
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd"> 2022-08-01T19:44:57.283422 image/svg+xml Matplotlib v3.5.2, https://matplotlib.org/
mitophagy_nodes.to_pickle('targets/mitophagy_GO.pickle')

Overlap

KEGG_GO_venn(mitophagy_brite_genes, mitophagy_nodes)
<matplotlib_venn._common.VennDiagram at 0x199e82f40>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd"> 2022-08-01T19:44:57.403791 image/svg+xml Matplotlib v3.5.2, https://matplotlib.org/

Lysosomal acidification


KEGG

lysosome_KEGG_pathway = 'hsa04142'
Image(REST.kegg_get(lysosome_KEGG_pathway, 'image').read())
lysosome_pathway_genes = get_KEGG_pathway_gene_members(lysosome_KEGG_pathway)
lysosome_pathway_genes.set_index('ENSG')['gene_name'].to_pickle('./targets/lysosome_kegg.pickle')

GO

lysosome_subgraph, lysosome_nodes = GO_subgraph_from_query('lysosom')
df = create_GO_by_gene_matrix(lysosome_nodes, attr='gene_name')
df = sort_df_by_hclust_olo(df)
ax = plot_gene_membership_in_GO_terms(df, figsize=(6, 10))
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd"> 2022-08-01T19:45:04.254706 image/svg+xml Matplotlib v3.5.2, https://matplotlib.org/
lysosome_nodes.to_pickle('targets/lysosome_GO.pickle')

Overlap

KEGG_GO_venn(lysosome_pathway_genes, lysosome_nodes)
<matplotlib_venn._common.VennDiagram at 0x199e873a0>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd"> 2022-08-01T19:45:07.914521 image/svg+xml Matplotlib v3.5.2, https://matplotlib.org/

Heterochromatin Defects

brite = 'ko03036'
brite_genes = get_KEGG_BRITE_entry(brite)
brite_genes = brite_genes.loc['Eukaryotic type']

TE de-repression


# Silencing chromatin modifiers,
# TFs which recognize ERVs

KEGG

gene_silencing_brite = brite_genes.loc['Gene silencing']
gene_silencing_brite.index = gene_silencing_brite.index.droplevel(2)
gene_silencing_brite.to_pickle('targets/gene_silencing_brite.pickle')

GO

transposon_subgraph, transposon_nodes = GO_subgraph_from_query('transpos')
draw_graph(transposon_subgraph)
transposition, RNA-mediated transposition, RNA-mediated transposition transposition transposition, RNA-mediated->transposition negative regulation of transposon integration negative regulation of transposon integration regulation of transposon integration regulation of transposon integration negative regulation of transposon integration->regulation of transposon integration negative regulation of transposition negative regulation of transposition negative regulation of transposon integration->negative regulation of transposition regulation of transposition regulation of transposition regulation of transposon integration->regulation of transposition negative regulation of transposition->regulation of transposition regulation of transposition, DNA-mediated regulation of transposition, DNA-mediated regulation of transposition, DNA-mediated->regulation of transposition positive regulation of transposition positive regulation of transposition positive regulation of transposition->regulation of transposition intramolecular oxidoreductase activity, transposing C=C bonds intramolecular oxidoreductase activity, transposing C=C bonds positive regulation of transposition, RNA-mediated positive regulation of transposition, RNA-mediated positive regulation of transposition, RNA-mediated->positive regulation of transposition regulation of transposition, RNA-mediated regulation of transposition, RNA-mediated positive regulation of transposition, RNA-mediated->regulation of transposition, RNA-mediated regulation of transposition, RNA-mediated->regulation of transposition negative regulation of transposition, DNA-mediated negative regulation of transposition, DNA-mediated negative regulation of transposition, DNA-mediated->negative regulation of transposition negative regulation of transposition, DNA-mediated->regulation of transposition, DNA-mediated transposon integration involved in RNA-mediated transposition transposon integration involved in RNA-mediated transposition transposon integration involved in RNA-mediated transposition->transposition, RNA-mediated transposon integration transposon integration transposon integration involved in RNA-mediated transposition->transposon integration transposon integration->transposition replicative transposition, DNA-mediated replicative transposition, DNA-mediated transposition, DNA-mediated transposition, DNA-mediated replicative transposition, DNA-mediated->transposition, DNA-mediated transposition, DNA-mediated->transposition reverse transcription involved in RNA-mediated transposition reverse transcription involved in RNA-mediated transposition reverse transcription involved in RNA-mediated transposition->transposition, RNA-mediated positive regulation of transposon integration positive regulation of transposon integration positive regulation of transposon integration->regulation of transposon integration positive regulation of transposon integration->positive regulation of transposition MITE transposition MITE transposition MITE transposition->transposition negative regulation of transposition, RNA-mediated negative regulation of transposition, RNA-mediated negative regulation of transposition, RNA-mediated->negative regulation of transposition negative regulation of transposition, RNA-mediated->regulation of transposition, RNA-mediated non-replicative transposition, DNA-mediated non-replicative transposition, DNA-mediated non-replicative transposition, DNA-mediated->transposition, DNA-mediated retrotransposon nucleocapsid retrotransposon nucleocapsid positive regulation of transposition, DNA-mediated positive regulation of transposition, DNA-mediated positive regulation of transposition, DNA-mediated->regulation of transposition, DNA-mediated positive regulation of transposition, DNA-mediated->positive regulation of transposition intramolecular oxidoreductase activity, transposing S-S bonds intramolecular oxidoreductase activity, transposing S-S bonds transposase activity transposase activity
df = create_GO_by_gene_matrix(transposon_nodes, attr='gene_name')
df = sort_df_by_hclust_olo(df)
ax = plot_gene_membership_in_GO_terms(df, figsize=(6, 10))
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd"> 2022-08-01T19:45:10.122414 image/svg+xml Matplotlib v3.5.2, https://matplotlib.org/
transposon_nodes.to_pickle('targets/transposon_GO.pickle')

Overlap

KEGG_GO_venn(gene_silencing_brite, transposon_nodes)
<matplotlib_venn._common.VennDiagram at 0x1aa7fa670>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd"> 2022-08-01T19:45:10.307020 image/svg+xml Matplotlib v3.5.2, https://matplotlib.org/

Chromatin modifiers


KEGG

chromatin_remodeling_brite = brite_genes.loc['Chromatin remodeling factors']
chromatin_remodeling_brite.index = chromatin_remodeling_brite.index.droplevel(2).droplevel(1)
chromatin_remodeling_brite.to_pickle('targets/chromatin_remodeling_brite.pickle')
histone_modification_brite = brite_genes.loc['Histone modification proteins']
histone_modification_brite = drop_nan_index_levels(histone_modification_brite)
histone_modification_brite.to_pickle('targets/histone_modification_brite.pickle')

GO

chromatin_remodeling_subgraph, chromatin_remodeling_nodes = GO_subgraph_from_query('chromatin remodel')
draw_graph(chromatin_remodeling_subgraph)
chromatin remodeling at centromere chromatin remodeling at centromere chromatin remodeling chromatin remodeling chromatin remodeling at centromere->chromatin remodeling DNA repair-dependent chromatin remodeling DNA repair-dependent chromatin remodeling DNA repair-dependent chromatin remodeling->chromatin remodeling ATP-dependent chromatin remodeler activity ATP-dependent chromatin remodeler activity
chromatin_remodeling_nodes.to_pickle('targets/chromatin_remodeling_GO.pickle')

Overlap

KEGG_GO_venn(chromatin_remodeling_brite, chromatin_remodeling_nodes)
<matplotlib_venn._common.VennDiagram at 0x1a9343df0>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd"> 2022-08-01T19:45:10.536337 image/svg+xml Matplotlib v3.5.2, https://matplotlib.org/

Epigenetic Erosion (heterochromatin loosening)


KEGG

heterochromatin_formation_brite = brite_genes.loc['Heterochromatin formation proteins']
heterochromatin_formation_brite = drop_nan_index_levels(heterochromatin_formation_brite)
heterochromatin_formation_brite.to_pickle('targets/heterochromatin_formation_brite.pickle')

GO

heterochromatin_subgraph, heterochromatin_nodes = GO_subgraph_from_query('heterochromatin')
draw_graph(heterochromatin_subgraph)
meiotic attachment of telomeric heterochromatin to spindle pole body meiotic attachment of telomeric heterochromatin to spindle pole body negative regulation of heterochromatin organization negative regulation of heterochromatin organization regulation of heterochromatin organization regulation of heterochromatin organization negative regulation of heterochromatin organization->regulation of heterochromatin organization siRNA-dependent facultative heterochromatin formation siRNA-dependent facultative heterochromatin formation small non-coding RNA-dependent heterochromatin formation small non-coding RNA-dependent heterochromatin formation siRNA-dependent facultative heterochromatin formation->small non-coding RNA-dependent heterochromatin formation heterochromatin formation heterochromatin formation small non-coding RNA-dependent heterochromatin formation->heterochromatin formation alpha-heterochromatin alpha-heterochromatin pericentric heterochromatin pericentric heterochromatin alpha-heterochromatin->pericentric heterochromatin heterochromatin heterochromatin pericentric heterochromatin->heterochromatin beta-heterochromatin beta-heterochromatin beta-heterochromatin->pericentric heterochromatin regulation of rDNA heterochromatin formation regulation of rDNA heterochromatin formation regulation of heterochromatin formation regulation of heterochromatin formation regulation of rDNA heterochromatin formation->regulation of heterochromatin formation regulation of heterochromatin formation->regulation of heterochromatin organization protein localization to pericentric heterochromatin protein localization to pericentric heterochromatin protein localization to heterochromatin protein localization to heterochromatin protein localization to pericentric heterochromatin->protein localization to heterochromatin regulation of siRNA-dependent facultative heterochromatin formation regulation of siRNA-dependent facultative heterochromatin formation regulation of small non-coding RNA-mediated heterochromatin formation regulation of small non-coding RNA-mediated heterochromatin formation regulation of siRNA-dependent facultative heterochromatin formation->regulation of small non-coding RNA-mediated heterochromatin formation regulation of small non-coding RNA-mediated heterochromatin formation->regulation of heterochromatin formation protein localization to mating-type region heterochromatin protein localization to mating-type region heterochromatin protein localization to mating-type region heterochromatin->protein localization to heterochromatin silent mating-type cassette heterochromatin formation silent mating-type cassette heterochromatin formation constitutive heterochromatin formation constitutive heterochromatin formation silent mating-type cassette heterochromatin formation->constitutive heterochromatin formation constitutive heterochromatin formation->heterochromatin formation nucleolus-associated heterochromatin nucleolus-associated heterochromatin negative regulation of heterochromatin formation negative regulation of heterochromatin formation negative regulation of heterochromatin formation->negative regulation of heterochromatin organization negative regulation of heterochromatin formation->regulation of heterochromatin formation heterochromatin organization heterochromatin organization heterochromatin formation->heterochromatin organization rDNA heterochromatin formation rDNA heterochromatin formation facultative heterochromatin formation facultative heterochromatin formation rDNA heterochromatin formation->facultative heterochromatin formation facultative heterochromatin formation->heterochromatin formation inactivation of X chromosome by heterochromatin formation inactivation of X chromosome by heterochromatin formation inactivation of X chromosome by heterochromatin formation->constitutive heterochromatin formation subtelomeric heterochromatin formation subtelomeric heterochromatin formation subtelomeric heterochromatin formation->constitutive heterochromatin formation siRNA-dependent pericentric heterochromatin formation siRNA-dependent pericentric heterochromatin formation pericentric heterochromatin formation pericentric heterochromatin formation siRNA-dependent pericentric heterochromatin formation->pericentric heterochromatin formation pericentric heterochromatin formation->constitutive heterochromatin formation regulation of silent mating-type cassette heterochromatin formation regulation of silent mating-type cassette heterochromatin formation regulation of silent mating-type cassette heterochromatin formation->regulation of heterochromatin formation maintenance of protein localization to heterochromatin maintenance of protein localization to heterochromatin maintenance of protein localization to heterochromatin->protein localization to heterochromatin protein localization to subtelomeric heterochromatin protein localization to subtelomeric heterochromatin protein localization to subtelomeric heterochromatin->protein localization to heterochromatin heterochromatin domain heterochromatin domain heterochromatin domain->heterochromatin positive regulation of DNA methylation-dependent heterochromatin formation positive regulation of DNA methylation-dependent heterochromatin formation positive regulation of heterochromatin formation positive regulation of heterochromatin formation positive regulation of DNA methylation-dependent heterochromatin formation->positive regulation of heterochromatin formation regulation of DNA methylation-dependent heterochromatin formation regulation of DNA methylation-dependent heterochromatin formation positive regulation of DNA methylation-dependent heterochromatin formation->regulation of DNA methylation-dependent heterochromatin formation positive regulation of heterochromatin formation->regulation of heterochromatin formation positive regulation of heterochromatin organization positive regulation of heterochromatin organization positive regulation of heterochromatin formation->positive regulation of heterochromatin organization regulation of DNA methylation-dependent heterochromatin formation->regulation of heterochromatin formation regulation of siRNA-independent facultative heterochromatin formation regulation of siRNA-independent facultative heterochromatin formation regulation of siRNA-independent facultative heterochromatin formation->regulation of heterochromatin formation negative regulation of DNA methylation-dependent heterochromatin formation negative regulation of DNA methylation-dependent heterochromatin formation negative regulation of DNA methylation-dependent heterochromatin formation->negative regulation of heterochromatin formation negative regulation of DNA methylation-dependent heterochromatin formation->regulation of DNA methylation-dependent heterochromatin formation positive regulation of rDNA heterochromatin formation positive regulation of rDNA heterochromatin formation positive regulation of rDNA heterochromatin formation->regulation of rDNA heterochromatin formation positive regulation of rDNA heterochromatin formation->positive regulation of heterochromatin formation heterochromatin-nuclear membrane anchor activity heterochromatin-nuclear membrane anchor activity pericentric heterochromatin organization pericentric heterochromatin organization pericentric heterochromatin organization->heterochromatin formation mating-type region heterochromatin mating-type region heterochromatin mating-type region heterochromatin->heterochromatin positive regulation of pericentric heterochromatin formation positive regulation of pericentric heterochromatin formation positive regulation of pericentric heterochromatin formation->positive regulation of heterochromatin formation regulation of pericentric heterochromatin formation regulation of pericentric heterochromatin formation positive regulation of pericentric heterochromatin formation->regulation of pericentric heterochromatin formation regulation of pericentric heterochromatin formation->regulation of heterochromatin formation intercalary heterochromatin intercalary heterochromatin intercalary heterochromatin->heterochromatin positive regulation of heterochromatin organization->regulation of heterochromatin organization CLRC complex localization to heterochromatin CLRC complex localization to heterochromatin CLRC complex localization to heterochromatin->protein localization to heterochromatin positive regulation of silent mating-type cassette heterochromatin formation positive regulation of silent mating-type cassette heterochromatin formation positive regulation of silent mating-type cassette heterochromatin formation->regulation of silent mating-type cassette heterochromatin formation positive regulation of silent mating-type cassette heterochromatin formation->positive regulation of heterochromatin formation senescence-associated heterochromatin focus senescence-associated heterochromatin focus senescence-associated heterochromatin focus->heterochromatin siRNA-independent facultative heterochromatin formation siRNA-independent facultative heterochromatin formation siRNA-independent facultative heterochromatin formation->facultative heterochromatin formation heterochromatin island heterochromatin island heterochromatin island->heterochromatin heterochromatin boundary formation heterochromatin boundary formation heterochromatin boundary formation->heterochromatin formation heterochromatin boundary formation->heterochromatin organization DNA methylation-dependent heterochromatin formation DNA methylation-dependent heterochromatin formation DNA methylation-dependent heterochromatin formation->facultative heterochromatin formation negative regulation of ribosomal DNA heterochromatin formation negative regulation of ribosomal DNA heterochromatin formation negative regulation of ribosomal DNA heterochromatin formation->regulation of rDNA heterochromatin formation negative regulation of ribosomal DNA heterochromatin formation->negative regulation of heterochromatin formation attachment of telomeric heterochromatin to nuclear envelope attachment of telomeric heterochromatin to nuclear envelope silent mating-type cassette heterochromatin organization silent mating-type cassette heterochromatin organization silent mating-type cassette heterochromatin organization->constitutive heterochromatin formation negative regulation of silent mating-type cassette heterochromatin formation negative regulation of silent mating-type cassette heterochromatin formation negative regulation of silent mating-type cassette heterochromatin formation->negative regulation of heterochromatin formation negative regulation of silent mating-type cassette heterochromatin formation->regulation of silent mating-type cassette heterochromatin formation subtelomeric heterochromatin subtelomeric heterochromatin subtelomeric heterochromatin->heterochromatin negative regulation of small non-coding RNA-mediated heterochromatin formation negative regulation of small non-coding RNA-mediated heterochromatin formation negative regulation of small non-coding RNA-mediated heterochromatin formation->regulation of small non-coding RNA-mediated heterochromatin formation negative regulation of small non-coding RNA-mediated heterochromatin formation->negative regulation of heterochromatin formation rDNA heterochromatin rDNA heterochromatin rDNA heterochromatin->heterochromatin
heterochromatin_nodes.to_pickle('targets/heterochromatin_GO.pickle')

Overlap

KEGG_GO_venn(heterochromatin_formation_brite, heterochromatin_nodes)
<matplotlib_venn._common.VennDiagram at 0x1a96a5df0>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd"> 2022-08-01T19:45:10.771697 image/svg+xml Matplotlib v3.5.2, https://matplotlib.org/

histones are limiting


KEGG

nucleosome_assembly_brite = brite_genes.loc['Nucleosome assembly factors']
nucleosome_assembly_brite = drop_nan_index_levels(nucleosome_assembly_brite)
nucleosome_assembly_brite.to_pickle('targets/nucleosome_assembly_brite.pickle')

GO

nucleosome_assembly_subgraph, nucleosome_assembly_nodes = GO_subgraph_from_query('nucleosome assembly')
draw_graph(nucleosome_assembly_subgraph)
nucleosome assembly nucleosome assembly
nucleosome_assembly_nodes.to_pickle('targets/nucleosome_assembly_GO.pickle')

Overlap

KEGG_GO_venn(nucleosome_assembly_brite, nucleosome_assembly_nodes)
<matplotlib_venn._common.VennDiagram at 0x1a925ffd0>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd"> 2022-08-01T19:45:10.982377 image/svg+xml Matplotlib v3.5.2, https://matplotlib.org/

Nuclear Lamin defects


Image('https://upload.wikimedia.org/wikipedia/commons/b/b4/Structure_and_function_of_the_nuclear_lamina.jpg')

KEGG

nuclear_lamin_brite_id = 'ko04812+K12641'
nuclear_lamin_brite = get_KEGG_BRITE_entry(nuclear_lamin_brite_id)
nuclear_lamin_brite = nuclear_lamin_brite.loc['Eukaryotic cytoskeleton proteins', 'Intermediate filaments', 'Intermediate filaments', 'Type V: Nuclear lamins']
nuclear_lamin_brite.index = ['Nuclear lamins']*len(nuclear_lamin_brite)
/var/folders/mq/yzq45gh52xn7zz498z7cjtkw0000gn/T/ipykernel_10928/5367033.py:1: PerformanceWarning: indexing past lexsort depth may impact performance.
  nuclear_lamin_brite = nuclear_lamin_brite.loc['Eukaryotic cytoskeleton proteins', 'Intermediate filaments', 'Intermediate filaments', 'Type V: Nuclear lamins']
nuclear_lamin_brite.to_pickle('targets/nuclear_lamin_brite.pickle')

GO

nuclear_lamin_subgraph, nuclear_lamin_nodes = GO_subgraph_from_query('nuclear lamin')
draw_graph(nuclear_lamin_subgraph)
nuclear lamina nuclear lamina host cell nuclear lamina host cell nuclear lamina
nuclear_lamin_nodes.to_pickle('targets/nuclear_lamin_GO.pickle')

Overlap

KEGG_GO_venn(nuclear_lamin_brite, nuclear_lamin_nodes)
<matplotlib_venn._common.VennDiagram at 0x1a9d43bb0>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd"> 2022-08-01T19:45:12.529306 image/svg+xml Matplotlib v3.5.2, https://matplotlib.org/

neurons entering cell cycle? Cell cycle markers


KEGG

cell_cycle_pathway_id = 'hsa04110'
Image(REST.kegg_get(cell_cycle_pathway_id, 'image').read())
cell_cycle_pathway_genes = get_KEGG_pathway_gene_members(cell_cycle_pathway_id)
cell_cycle_pathway_genes.to_pickle('cell_cycle_pathway.pickle')

GO

cell_cycle_subgraph, cell_cycle_nodes = GO_subgraph_from_query('cell cycle')
df = create_GO_by_gene_matrix(cell_cycle_nodes, attr='gene_name')
df = sort_df_by_hclust_olo(df)

matplotlib_inline.backend_inline.set_matplotlib_formats('png')
ax = plot_gene_membership_in_GO_terms(df, figsize=(6, 10))
draw_graph(cell_cycle_subgraph)
regulation of transcription involved in G1/S transition of mitotic cell cycle regulation of transcription involved in G1/S transition of mitotic cell cycle mitotic cell cycle process mitotic cell cycle process regulation of transcription involved in G1/S transition of mitotic cell cycle->mitotic cell cycle process G1/S transition of mitotic cell cycle G1/S transition of mitotic cell cycle regulation of transcription involved in G1/S transition of mitotic cell cycle->G1/S transition of mitotic cell cycle mitotic cell cycle mitotic cell cycle mitotic cell cycle process->mitotic cell cycle cell cycle process cell cycle process mitotic cell cycle process->cell cycle process cell cycle G1/S phase transition cell cycle G1/S phase transition G1/S transition of mitotic cell cycle->cell cycle G1/S phase transition mitotic cell cycle phase transition mitotic cell cycle phase transition G1/S transition of mitotic cell cycle->mitotic cell cycle phase transition meiotic cell cycle checkpoint signaling meiotic cell cycle checkpoint signaling cell cycle checkpoint signaling cell cycle checkpoint signaling meiotic cell cycle checkpoint signaling->cell cycle checkpoint signaling meiotic cell cycle process meiotic cell cycle process meiotic cell cycle checkpoint signaling->meiotic cell cycle process negative regulation of cell cycle phase transition negative regulation of cell cycle phase transition cell cycle checkpoint signaling->negative regulation of cell cycle phase transition meiotic cell cycle process->cell cycle process meiotic cell cycle meiotic cell cycle meiotic cell cycle process->meiotic cell cycle mitotic cell cycle, embryonic mitotic cell cycle, embryonic mitotic cell cycle, embryonic->mitotic cell cycle cell cycle cell cycle mitotic cell cycle->cell cycle regulation of mitotic cell cycle, embryonic regulation of mitotic cell cycle, embryonic regulation of mitotic cell cycle regulation of mitotic cell cycle regulation of mitotic cell cycle, embryonic->regulation of mitotic cell cycle regulation of cell cycle regulation of cell cycle regulation of mitotic cell cycle->regulation of cell cycle meiosis II cell cycle process meiosis II cell cycle process meiosis II cell cycle process->meiotic cell cycle process mitotic cell cycle checkpoint signaling mitotic cell cycle checkpoint signaling mitotic cell cycle checkpoint signaling->mitotic cell cycle process mitotic cell cycle checkpoint signaling->cell cycle checkpoint signaling negative regulation of mitotic cell cycle negative regulation of mitotic cell cycle mitotic cell cycle checkpoint signaling->negative regulation of mitotic cell cycle negative regulation of mitotic cell cycle->regulation of mitotic cell cycle negative regulation of cell cycle negative regulation of cell cycle negative regulation of mitotic cell cycle->negative regulation of cell cycle positive regulation of cell cycle switching, mitotic to meiotic cell cycle positive regulation of cell cycle switching, mitotic to meiotic cell cycle positive regulation of cell cycle process positive regulation of cell cycle process positive regulation of cell cycle switching, mitotic to meiotic cell cycle->positive regulation of cell cycle process positive regulation of meiotic cell cycle positive regulation of meiotic cell cycle positive regulation of cell cycle switching, mitotic to meiotic cell cycle->positive regulation of meiotic cell cycle regulation of cell cycle switching, mitotic to meiotic cell cycle regulation of cell cycle switching, mitotic to meiotic cell cycle positive regulation of cell cycle switching, mitotic to meiotic cell cycle->regulation of cell cycle switching, mitotic to meiotic cell cycle regulation of cell cycle process regulation of cell cycle process positive regulation of cell cycle process->regulation of cell cycle process positive regulation of cell cycle positive regulation of cell cycle positive regulation of cell cycle process->positive regulation of cell cycle positive regulation of meiotic cell cycle->positive regulation of cell cycle regulation of meiotic cell cycle regulation of meiotic cell cycle positive regulation of meiotic cell cycle->regulation of meiotic cell cycle regulation of cell cycle switching, mitotic to meiotic cell cycle->regulation of mitotic cell cycle regulation of cell cycle switching, mitotic to meiotic cell cycle->regulation of cell cycle process regulation of cell cycle switching, mitotic to meiotic cell cycle->regulation of meiotic cell cycle negative regulation of G1/S transition of mitotic cell cycle negative regulation of G1/S transition of mitotic cell cycle negative regulation of mitotic cell cycle phase transition negative regulation of mitotic cell cycle phase transition negative regulation of G1/S transition of mitotic cell cycle->negative regulation of mitotic cell cycle phase transition regulation of G1/S transition of mitotic cell cycle regulation of G1/S transition of mitotic cell cycle negative regulation of G1/S transition of mitotic cell cycle->regulation of G1/S transition of mitotic cell cycle negative regulation of cell cycle G1/S phase transition negative regulation of cell cycle G1/S phase transition negative regulation of G1/S transition of mitotic cell cycle->negative regulation of cell cycle G1/S phase transition negative regulation of mitotic cell cycle phase transition->negative regulation of mitotic cell cycle negative regulation of mitotic cell cycle phase transition->negative regulation of cell cycle phase transition regulation of mitotic cell cycle phase transition regulation of mitotic cell cycle phase transition negative regulation of mitotic cell cycle phase transition->regulation of mitotic cell cycle phase transition regulation of G1/S transition of mitotic cell cycle->regulation of mitotic cell cycle phase transition regulation of cell cycle G1/S phase transition regulation of cell cycle G1/S phase transition regulation of G1/S transition of mitotic cell cycle->regulation of cell cycle G1/S phase transition negative regulation of cell cycle G1/S phase transition->negative regulation of cell cycle phase transition negative regulation of cell cycle G1/S phase transition->regulation of cell cycle G1/S phase transition meiotic cell cycle phase meiotic cell cycle phase cell cycle phase cell cycle phase meiotic cell cycle phase->cell cycle phase response to cell cycle checkpoint signaling response to cell cycle checkpoint signaling signal transduction involved in cell cycle switching, mitotic to meiotic cell cycle signal transduction involved in cell cycle switching, mitotic to meiotic cell cycle cell cycle switching, mitotic to meiotic cell cycle cell cycle switching, mitotic to meiotic cell cycle signal transduction involved in cell cycle switching, mitotic to meiotic cell cycle->cell cycle switching, mitotic to meiotic cell cycle signal transduction involved in cell cycle switching, mitotic to meiotic cell cycle->cell cycle process cell cycle switching, mitotic to meiotic cell cycle->negative regulation of mitotic cell cycle cell cycle switching, mitotic to meiotic cell cycle->positive regulation of meiotic cell cycle cell cycle switching cell cycle switching cell cycle switching, mitotic to meiotic cell cycle->cell cycle switching cell cycle process->cell cycle positive regulation of response to cell cycle checkpoint signaling positive regulation of response to cell cycle checkpoint signaling regulation of response to cell cycle checkpoint signaling regulation of response to cell cycle checkpoint signaling positive regulation of response to cell cycle checkpoint signaling->regulation of response to cell cycle checkpoint signaling endomitotic cell cycle endomitotic cell cycle endomitotic cell cycle->mitotic cell cycle positive regulation of syncytial blastoderm mitotic cell cycle positive regulation of syncytial blastoderm mitotic cell cycle positive regulation of mitotic cell cycle, embryonic positive regulation of mitotic cell cycle, embryonic positive regulation of syncytial blastoderm mitotic cell cycle->positive regulation of mitotic cell cycle, embryonic regulation of syncytial blastoderm mitotic cell cycle regulation of syncytial blastoderm mitotic cell cycle positive regulation of syncytial blastoderm mitotic cell cycle->regulation of syncytial blastoderm mitotic cell cycle positive regulation of mitotic cell cycle, embryonic->regulation of mitotic cell cycle, embryonic positive regulation of mitotic cell cycle positive regulation of mitotic cell cycle positive regulation of mitotic cell cycle, embryonic->positive regulation of mitotic cell cycle regulation of syncytial blastoderm mitotic cell cycle->regulation of mitotic cell cycle, embryonic regulation of syncytial blastoderm mitotic cell cycle->cell cycle process regulation of cell cycle process->regulation of cell cycle negative regulation of metaphase/anaphase transition of cell cycle negative regulation of metaphase/anaphase transition of cell cycle regulation of metaphase/anaphase transition of cell cycle regulation of metaphase/anaphase transition of cell cycle negative regulation of metaphase/anaphase transition of cell cycle->regulation of metaphase/anaphase transition of cell cycle negative regulation of metaphase/anaphase transition of cell cycle->negative regulation of cell cycle phase transition regulation of cell cycle phase transition regulation of cell cycle phase transition regulation of metaphase/anaphase transition of cell cycle->regulation of cell cycle phase transition negative regulation of cell cycle phase transition->regulation of cell cycle phase transition negative regulation of cell cycle process negative regulation of cell cycle process negative regulation of cell cycle phase transition->negative regulation of cell cycle process cell cycle DNA replication DNA unwinding cell cycle DNA replication DNA unwinding cell cycle DNA replication DNA unwinding->cell cycle process cell cycle DNA replication cell cycle DNA replication cell cycle DNA replication DNA unwinding->cell cycle DNA replication cell cycle DNA replication->cell cycle process positive regulation of metaphase/anaphase transition of meiotic cell cycle positive regulation of metaphase/anaphase transition of meiotic cell cycle regulation of metaphase/anaphase transition of meiotic cell cycle regulation of metaphase/anaphase transition of meiotic cell cycle positive regulation of metaphase/anaphase transition of meiotic cell cycle->regulation of metaphase/anaphase transition of meiotic cell cycle positive regulation of metaphase/anaphase transition of cell cycle positive regulation of metaphase/anaphase transition of cell cycle positive regulation of metaphase/anaphase transition of meiotic cell cycle->positive regulation of metaphase/anaphase transition of cell cycle positive regulation of meiotic cell cycle phase transition positive regulation of meiotic cell cycle phase transition positive regulation of metaphase/anaphase transition of meiotic cell cycle->positive regulation of meiotic cell cycle phase transition regulation of metaphase/anaphase transition of meiotic cell cycle->regulation of metaphase/anaphase transition of cell cycle regulation of meiotic cell cycle phase transition regulation of meiotic cell cycle phase transition regulation of metaphase/anaphase transition of meiotic cell cycle->regulation of meiotic cell cycle phase transition positive regulation of metaphase/anaphase transition of cell cycle->regulation of metaphase/anaphase transition of cell cycle positive regulation of cell cycle phase transition positive regulation of cell cycle phase transition positive regulation of metaphase/anaphase transition of cell cycle->positive regulation of cell cycle phase transition positive regulation of meiotic cell cycle phase transition->positive regulation of meiotic cell cycle positive regulation of meiotic cell cycle phase transition->regulation of meiotic cell cycle phase transition positive regulation of meiotic cell cycle phase transition->positive regulation of cell cycle phase transition cell cycle switching->cell cycle process regulation of cell cycle phase transition->regulation of cell cycle process DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest positive regulation of G2/MI transition of meiotic cell cycle positive regulation of G2/MI transition of meiotic cell cycle positive regulation of G2/MI transition of meiotic cell cycle->positive regulation of meiotic cell cycle phase transition regulation of G2/MI transition of meiotic cell cycle regulation of G2/MI transition of meiotic cell cycle positive regulation of G2/MI transition of meiotic cell cycle->regulation of G2/MI transition of meiotic cell cycle positive regulation of cell cycle G2/M phase transition positive regulation of cell cycle G2/M phase transition positive regulation of G2/MI transition of meiotic cell cycle->positive regulation of cell cycle G2/M phase transition regulation of G2/MI transition of meiotic cell cycle->regulation of meiotic cell cycle phase transition regulation of cell cycle G2/M phase transition regulation of cell cycle G2/M phase transition regulation of G2/MI transition of meiotic cell cycle->regulation of cell cycle G2/M phase transition positive regulation of cell cycle G2/M phase transition->regulation of cell cycle G2/M phase transition positive regulation of cell cycle G2/M phase transition->positive regulation of cell cycle phase transition traversing start control point of mitotic cell cycle traversing start control point of mitotic cell cycle positive regulation of G1/S transition of mitotic cell cycle positive regulation of G1/S transition of mitotic cell cycle traversing start control point of mitotic cell cycle->positive regulation of G1/S transition of mitotic cell cycle positive regulation of G1/S transition of mitotic cell cycle->regulation of G1/S transition of mitotic cell cycle positive regulation of mitotic cell cycle phase transition positive regulation of mitotic cell cycle phase transition positive regulation of G1/S transition of mitotic cell cycle->positive regulation of mitotic cell cycle phase transition positive regulation of cell cycle G1/S phase transition positive regulation of cell cycle G1/S phase transition positive regulation of G1/S transition of mitotic cell cycle->positive regulation of cell cycle G1/S phase transition meiotic cell cycle phase transition meiotic cell cycle phase transition meiotic cell cycle phase transition->meiotic cell cycle process cell cycle phase transition cell cycle phase transition meiotic cell cycle phase transition->cell cycle phase transition cell cycle phase transition->cell cycle process re-entry into mitotic cell cycle after pheromone arrest re-entry into mitotic cell cycle after pheromone arrest re-entry into mitotic cell cycle re-entry into mitotic cell cycle re-entry into mitotic cell cycle after pheromone arrest->re-entry into mitotic cell cycle re-entry into mitotic cell cycle->cell cycle process positive regulation of cell cycle->regulation of cell cycle cell cycle comprising mitosis without cytokinesis cell cycle comprising mitosis without cytokinesis cell cycle comprising mitosis without cytokinesis->mitotic cell cycle G2/MI transition of meiotic cell cycle G2/MI transition of meiotic cell cycle G2/MI transition of meiotic cell cycle->meiotic cell cycle phase transition meiosis I cell cycle process meiosis I cell cycle process G2/MI transition of meiotic cell cycle->meiosis I cell cycle process cell cycle G2/M phase transition cell cycle G2/M phase transition G2/MI transition of meiotic cell cycle->cell cycle G2/M phase transition meiosis I cell cycle process->meiotic cell cycle process cell cycle G2/M phase transition->cell cycle phase transition activation of mitotic cell cycle spindle assembly checkpoint activation of mitotic cell cycle spindle assembly checkpoint positive regulation of mitotic cell cycle spindle assembly checkpoint positive regulation of mitotic cell cycle spindle assembly checkpoint activation of mitotic cell cycle spindle assembly checkpoint->positive regulation of mitotic cell cycle spindle assembly checkpoint positive regulation of mitotic cell cycle spindle assembly checkpoint->positive regulation of cell cycle process regulation of mitotic cell cycle spindle assembly checkpoint regulation of mitotic cell cycle spindle assembly checkpoint positive regulation of mitotic cell cycle spindle assembly checkpoint->regulation of mitotic cell cycle spindle assembly checkpoint suppression by virus of G2/M transition of host mitotic cell cycle suppression by virus of G2/M transition of host mitotic cell cycle modulation by virus of host cell cycle modulation by virus of host cell cycle suppression by virus of G2/M transition of host mitotic cell cycle->modulation by virus of host cell cycle modification by virus of host cell cycle regulation modification by virus of host cell cycle regulation modulation by virus of host cell cycle->modification by virus of host cell cycle regulation metaphase/anaphase transition of cell cycle metaphase/anaphase transition of cell cycle metaphase/anaphase transition of cell cycle->cell cycle phase transition response to mitotic cell cycle checkpoint signaling response to mitotic cell cycle checkpoint signaling response to mitotic cell cycle checkpoint signaling->response to cell cycle checkpoint signaling negative regulation of G1/S transition of mitotic cell cycle by negative regulation of transcription from RNA polymerase II promoter negative regulation of G1/S transition of mitotic cell cycle by negative regulation of transcription from RNA polymerase II promoter negative regulation of G1/S transition of mitotic cell cycle by negative regulation of transcription from RNA polymerase II promoter->negative regulation of G1/S transition of mitotic cell cycle regulation of nuclear cell cycle DNA replication regulation of nuclear cell cycle DNA replication regulation of nuclear cell cycle DNA replication->regulation of cell cycle process regulation of meiotic cell cycle phase transition->regulation of cell cycle phase transition positive regulation of cell cycle checkpoint positive regulation of cell cycle checkpoint regulation of cell cycle checkpoint regulation of cell cycle checkpoint positive regulation of cell cycle checkpoint->regulation of cell cycle checkpoint regulation of cell cycle checkpoint->regulation of cell cycle phase transition negative regulation of nuclear cell cycle DNA replication negative regulation of nuclear cell cycle DNA replication negative regulation of nuclear cell cycle DNA replication->regulation of nuclear cell cycle DNA replication negative regulation of nuclear cell cycle DNA replication->negative regulation of cell cycle process negative regulation of cell cycle process->regulation of cell cycle process negative regulation of cell cycle process->negative regulation of cell cycle positive regulation of G2/M transition of mitotic cell cycle positive regulation of G2/M transition of mitotic cell cycle positive regulation of G2/M transition of mitotic cell cycle->positive regulation of cell cycle G2/M phase transition regulation of G2/M transition of mitotic cell cycle regulation of G2/M transition of mitotic cell cycle positive regulation of G2/M transition of mitotic cell cycle->regulation of G2/M transition of mitotic cell cycle positive regulation of G2/M transition of mitotic cell cycle->positive regulation of mitotic cell cycle phase transition regulation of G2/M transition of mitotic cell cycle->regulation of cell cycle G2/M phase transition regulation of G2/M transition of mitotic cell cycle->regulation of mitotic cell cycle phase transition positive regulation of mitotic cell cycle phase transition->regulation of mitotic cell cycle phase transition positive regulation of mitotic cell cycle phase transition->positive regulation of cell cycle phase transition positive regulation of mitotic cell cycle phase transition->positive regulation of mitotic cell cycle mitotic cell cycle G1 arrest in response to pheromone mitotic cell cycle G1 arrest in response to pheromone mitotic cell cycle G1 arrest in response to pheromone->negative regulation of mitotic cell cycle negative regulation of metaphase/anaphase transition of meiotic cell cycle negative regulation of metaphase/anaphase transition of meiotic cell cycle negative regulation of metaphase/anaphase transition of meiotic cell cycle->negative regulation of metaphase/anaphase transition of cell cycle negative regulation of metaphase/anaphase transition of meiotic cell cycle->regulation of metaphase/anaphase transition of meiotic cell cycle negative regulation of meiotic cell cycle phase transition negative regulation of meiotic cell cycle phase transition negative regulation of metaphase/anaphase transition of meiotic cell cycle->negative regulation of meiotic cell cycle phase transition negative regulation of meiotic cell cycle phase transition->negative regulation of cell cycle phase transition negative regulation of meiotic cell cycle phase transition->regulation of meiotic cell cycle phase transition negative regulation of meiotic cell cycle negative regulation of meiotic cell cycle negative regulation of meiotic cell cycle phase transition->negative regulation of meiotic cell cycle regulation of cell cycle G2/M phase transition->regulation of cell cycle phase transition regulation of mitotic cell cycle phase transition->regulation of mitotic cell cycle regulation of mitotic cell cycle phase transition->regulation of cell cycle phase transition positive regulation of cell cycle phase transition->positive regulation of cell cycle process positive regulation of cell cycle phase transition->regulation of cell cycle phase transition negative regulation of mitotic cell cycle DNA replication negative regulation of mitotic cell cycle DNA replication negative regulation of mitotic cell cycle DNA replication->negative regulation of mitotic cell cycle negative regulation of mitotic cell cycle DNA replication->negative regulation of nuclear cell cycle DNA replication regulation of mitotic cell cycle DNA replication regulation of mitotic cell cycle DNA replication negative regulation of mitotic cell cycle DNA replication->regulation of mitotic cell cycle DNA replication regulation of mitotic cell cycle DNA replication->regulation of mitotic cell cycle regulation of mitotic cell cycle DNA replication->regulation of nuclear cell cycle DNA replication regulation of meiotic cell cycle->regulation of cell cycle regulation of preblastoderm mitotic cell cycle regulation of preblastoderm mitotic cell cycle regulation of preblastoderm mitotic cell cycle->regulation of mitotic cell cycle, embryonic negative regulation of cell cycle->regulation of cell cycle negative regulation of meiotic cell cycle process involved in oocyte maturation negative regulation of meiotic cell cycle process involved in oocyte maturation negative regulation of meiotic cell cycle process involved in oocyte maturation->negative regulation of cell cycle process negative regulation of meiotic cell cycle process involved in oocyte maturation->negative regulation of meiotic cell cycle regulation of meiotic cell cycle process involved in oocyte maturation regulation of meiotic cell cycle process involved in oocyte maturation negative regulation of meiotic cell cycle process involved in oocyte maturation->regulation of meiotic cell cycle process involved in oocyte maturation negative regulation of meiotic cell cycle->regulation of meiotic cell cycle negative regulation of meiotic cell cycle->negative regulation of cell cycle regulation of meiotic cell cycle process involved in oocyte maturation->regulation of cell cycle process germline cell cycle switching, mitotic to meiotic cell cycle germline cell cycle switching, mitotic to meiotic cell cycle germline cell cycle switching, mitotic to meiotic cell cycle->cell cycle switching, mitotic to meiotic cell cycle negative regulation of transcription involved in meiotic cell cycle negative regulation of transcription involved in meiotic cell cycle regulation of transcription involved in meiotic cell cycle regulation of transcription involved in meiotic cell cycle negative regulation of transcription involved in meiotic cell cycle->regulation of transcription involved in meiotic cell cycle regulation of transcription involved in meiotic cell cycle->meiotic cell cycle negative regulation of transcription from RNA polymerase II promoter involved in meiotic cell cycle negative regulation of transcription from RNA polymerase II promoter involved in meiotic cell cycle negative regulation of transcription from RNA polymerase II promoter involved in meiotic cell cycle->negative regulation of transcription involved in meiotic cell cycle regulation of transcription from RNA polymerase II promoter involved in meiotic cell cycle regulation of transcription from RNA polymerase II promoter involved in meiotic cell cycle negative regulation of transcription from RNA polymerase II promoter involved in meiotic cell cycle->regulation of transcription from RNA polymerase II promoter involved in meiotic cell cycle regulation of transcription from RNA polymerase II promoter involved in meiotic cell cycle->regulation of transcription involved in meiotic cell cycle negative regulation of cell cycle switching, mitotic to meiotic cell cycle negative regulation of cell cycle switching, mitotic to meiotic cell cycle negative regulation of cell cycle switching, mitotic to meiotic cell cycle->regulation of cell cycle switching, mitotic to meiotic cell cycle negative regulation of cell cycle switching, mitotic to meiotic cell cycle->negative regulation of cell cycle process negative regulation of cell cycle switching, mitotic to meiotic cell cycle->positive regulation of mitotic cell cycle positive regulation of mitotic cell cycle->regulation of mitotic cell cycle positive regulation of mitotic cell cycle->positive regulation of cell cycle response to meiotic cell cycle checkpoint signaling response to meiotic cell cycle checkpoint signaling response to meiotic cell cycle checkpoint signaling->response to cell cycle checkpoint signaling pre-replicative complex assembly involved in nuclear cell cycle DNA replication pre-replicative complex assembly involved in nuclear cell cycle DNA replication pre-replicative complex assembly involved in cell cycle DNA replication pre-replicative complex assembly involved in cell cycle DNA replication pre-replicative complex assembly involved in nuclear cell cycle DNA replication->pre-replicative complex assembly involved in cell cycle DNA replication pre-replicative complex assembly involved in cell cycle DNA replication->cell cycle process pre-replicative complex assembly involved in cell cycle DNA replication->cell cycle DNA replication syncytial blastoderm mitotic cell cycle syncytial blastoderm mitotic cell cycle syncytial blastoderm mitotic cell cycle->mitotic cell cycle, embryonic syncytial blastoderm mitotic cell cycle->cell cycle comprising mitosis without cytokinesis meiotic cell cycle->cell cycle synthesis of RNA primer involved in nuclear cell cycle DNA replication synthesis of RNA primer involved in nuclear cell cycle DNA replication synthesis of RNA primer involved in cell cycle DNA replication synthesis of RNA primer involved in cell cycle DNA replication synthesis of RNA primer involved in nuclear cell cycle DNA replication->synthesis of RNA primer involved in cell cycle DNA replication synthesis of RNA primer involved in cell cycle DNA replication->cell cycle process synthesis of RNA primer involved in cell cycle DNA replication->cell cycle DNA replication cell cycle G1/S phase transition->cell cycle phase transition abortive mitotic cell cycle abortive mitotic cell cycle abortive mitotic cell cycle->mitotic cell cycle DNA strand elongation involved in nuclear cell cycle DNA replication DNA strand elongation involved in nuclear cell cycle DNA replication DNA strand elongation involved in cell cycle DNA replication DNA strand elongation involved in cell cycle DNA replication DNA strand elongation involved in nuclear cell cycle DNA replication->DNA strand elongation involved in cell cycle DNA replication DNA strand elongation involved in cell cycle DNA replication->cell cycle process DNA strand elongation involved in cell cycle DNA replication->cell cycle DNA replication negative regulation by symbiont of host cell cycle negative regulation by symbiont of host cell cycle negative regulation by symbiont of host cell cycle->negative regulation of cell cycle process modulation by symbiont of host cell cycle modulation by symbiont of host cell cycle negative regulation by symbiont of host cell cycle->modulation by symbiont of host cell cycle modulation by symbiont of host cell cycle->regulation of cell cycle process G2/M transition of mitotic cell cycle G2/M transition of mitotic cell cycle G2/M transition of mitotic cell cycle->cell cycle G2/M phase transition G2/M transition of mitotic cell cycle->mitotic cell cycle phase transition mitotic cell cycle phase transition->mitotic cell cycle process mitotic cell cycle phase transition->cell cycle phase transition cell cycle DNA replication initiation cell cycle DNA replication initiation cell cycle DNA replication initiation->cell cycle process cell cycle DNA replication initiation->cell cycle DNA replication negative regulation of cell cycle checkpoint negative regulation of cell cycle checkpoint negative regulation of cell cycle checkpoint->regulation of cell cycle checkpoint negative regulation of cell cycle checkpoint->positive regulation of cell cycle phase transition chromosome organization involved in meiotic cell cycle chromosome organization involved in meiotic cell cycle chromosome organization involved in meiotic cell cycle->meiotic cell cycle process negative regulation of G2/MI transition of meiotic cell cycle negative regulation of G2/MI transition of meiotic cell cycle negative regulation of G2/MI transition of meiotic cell cycle->regulation of G2/MI transition of meiotic cell cycle negative regulation of G2/MI transition of meiotic cell cycle->negative regulation of meiotic cell cycle phase transition negative regulation of cell cycle G2/M phase transition negative regulation of cell cycle G2/M phase transition negative regulation of G2/MI transition of meiotic cell cycle->negative regulation of cell cycle G2/M phase transition negative regulation of cell cycle G2/M phase transition->negative regulation of cell cycle phase transition negative regulation of cell cycle G2/M phase transition->regulation of cell cycle G2/M phase transition positive regulation of transcription involved in G1/S transition of mitotic cell cycle positive regulation of transcription involved in G1/S transition of mitotic cell cycle positive regulation of transcription involved in G1/S transition of mitotic cell cycle->regulation of transcription involved in G1/S transition of mitotic cell cycle actin filament reorganization involved in cell cycle actin filament reorganization involved in cell cycle actin filament reorganization involved in cell cycle->cell cycle process negative regulation of transcription involved in G1/S transition of mitotic cell cycle negative regulation of transcription involved in G1/S transition of mitotic cell cycle negative regulation of transcription involved in G1/S transition of mitotic cell cycle->regulation of transcription involved in G1/S transition of mitotic cell cycle positive regulation of cell cycle G1/S phase transition->positive regulation of cell cycle phase transition positive regulation of cell cycle G1/S phase transition->regulation of cell cycle G1/S phase transition regulation of cell cycle G1/S phase transition->regulation of cell cycle phase transition meiosis II cell cycle phase meiosis II cell cycle phase meiosis II cell cycle phase->meiotic cell cycle phase suppression by virus of host cell cycle arrest suppression by virus of host cell cycle arrest suppression by virus of host cell cycle arrest->modification by virus of host cell cycle regulation modification by virus of host cell cycle regulation->modulation by symbiont of host cell cycle cell cycle DNA replication DNA ligation cell cycle DNA replication DNA ligation cell cycle DNA replication DNA ligation->cell cycle process cell cycle DNA replication DNA ligation->cell cycle DNA replication mitotic G2 cell cycle arrest in response to glucose starvation mitotic G2 cell cycle arrest in response to glucose starvation mitotic G2 cell cycle arrest in response to glucose starvation->regulation of cell cycle negative regulation of preblastoderm mitotic cell cycle negative regulation of preblastoderm mitotic cell cycle negative regulation of preblastoderm mitotic cell cycle->regulation of preblastoderm mitotic cell cycle negative regulation of mitotic cell cycle, embryonic negative regulation of mitotic cell cycle, embryonic negative regulation of preblastoderm mitotic cell cycle->negative regulation of mitotic cell cycle, embryonic negative regulation of mitotic cell cycle, embryonic->regulation of mitotic cell cycle, embryonic negative regulation of mitotic cell cycle, embryonic->negative regulation of mitotic cell cycle metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of mitotic cell cycle->metaphase/anaphase transition of cell cycle metaphase/anaphase transition of mitotic cell cycle->mitotic cell cycle phase transition negative regulation of G2/M transition of mitotic cell cycle negative regulation of G2/M transition of mitotic cell cycle negative regulation of G2/M transition of mitotic cell cycle->negative regulation of mitotic cell cycle phase transition negative regulation of G2/M transition of mitotic cell cycle->regulation of G2/M transition of mitotic cell cycle negative regulation of G2/M transition of mitotic cell cycle->negative regulation of cell cycle G2/M phase transition preblastoderm mitotic cell cycle preblastoderm mitotic cell cycle preblastoderm mitotic cell cycle->mitotic cell cycle, embryonic preblastoderm mitotic cell cycle->cell cycle comprising mitosis without cytokinesis nuclear cell cycle DNA replication initiation nuclear cell cycle DNA replication initiation nuclear cell cycle DNA replication initiation->cell cycle DNA replication initiation mitotic cell cycle phase mitotic cell cycle phase mitotic cell cycle phase->cell cycle phase positive regulation of nuclear cell cycle DNA replication positive regulation of nuclear cell cycle DNA replication positive regulation of nuclear cell cycle DNA replication->positive regulation of cell cycle process positive regulation of nuclear cell cycle DNA replication->regulation of nuclear cell cycle DNA replication negative regulation of transcription involved in G2/M transition of mitotic cell cycle negative regulation of transcription involved in G2/M transition of mitotic cell cycle regulation of transcription involved in G2/M transition of mitotic cell cycle regulation of transcription involved in G2/M transition of mitotic cell cycle negative regulation of transcription involved in G2/M transition of mitotic cell cycle->regulation of transcription involved in G2/M transition of mitotic cell cycle regulation of transcription involved in G2/M transition of mitotic cell cycle->mitotic cell cycle process regulation of transcription involved in G2/M transition of mitotic cell cycle->G2/M transition of mitotic cell cycle positive regulation of meiotic cell cycle process involved in oocyte maturation positive regulation of meiotic cell cycle process involved in oocyte maturation positive regulation of meiotic cell cycle process involved in oocyte maturation->positive regulation of cell cycle process positive regulation of meiotic cell cycle process involved in oocyte maturation->positive regulation of meiotic cell cycle positive regulation of meiotic cell cycle process involved in oocyte maturation->regulation of meiotic cell cycle process involved in oocyte maturation positive regulation of G2/M transition of mitotic cell cycle involved in cellular response to nitrogen starvation positive regulation of G2/M transition of mitotic cell cycle involved in cellular response to nitrogen starvation positive regulation of G2/M transition of mitotic cell cycle involved in cellular response to nitrogen starvation->positive regulation of G2/M transition of mitotic cell cycle positive regulation of preblastoderm mitotic cell cycle positive regulation of preblastoderm mitotic cell cycle positive regulation of preblastoderm mitotic cell cycle->positive regulation of mitotic cell cycle, embryonic positive regulation of preblastoderm mitotic cell cycle->regulation of preblastoderm mitotic cell cycle response to mitotic cell cycle spindle orientation checkpoint signaling response to mitotic cell cycle spindle orientation checkpoint signaling metaphase/anaphase transition of meiotic cell cycle metaphase/anaphase transition of meiotic cell cycle metaphase/anaphase transition of meiotic cell cycle->meiotic cell cycle phase transition metaphase/anaphase transition of meiotic cell cycle->metaphase/anaphase transition of cell cycle cell cycle DNA replication maintenance of fidelity cell cycle DNA replication maintenance of fidelity cell cycle DNA replication maintenance of fidelity->cell cycle process cell cycle DNA replication maintenance of fidelity->cell cycle DNA replication first cell cycle pseudocleavage first cell cycle pseudocleavage response to mitotic cell cycle spindle assembly checkpoint signaling response to mitotic cell cycle spindle assembly checkpoint signaling regulation of establishment of actomyosin contractile ring localization involved in mitotic cell cycle regulation of establishment of actomyosin contractile ring localization involved in mitotic cell cycle positive regulation of transcription involved in G2/M transition of mitotic cell cycle positive regulation of transcription involved in G2/M transition of mitotic cell cycle positive regulation of transcription involved in G2/M transition of mitotic cell cycle->regulation of transcription involved in G2/M transition of mitotic cell cycle meiosis I cell cycle phase meiosis I cell cycle phase meiosis I cell cycle phase->meiotic cell cycle phase positive regulation of mitotic cell cycle DNA replication positive regulation of mitotic cell cycle DNA replication positive regulation of mitotic cell cycle DNA replication->regulation of mitotic cell cycle DNA replication positive regulation of mitotic cell cycle DNA replication->positive regulation of mitotic cell cycle positive regulation of mitotic cell cycle DNA replication->positive regulation of nuclear cell cycle DNA replication positive regulation of transcription from RNA polymerase II promoter involved in meiotic cell cycle positive regulation of transcription from RNA polymerase II promoter involved in meiotic cell cycle positive regulation of transcription from RNA polymerase II promoter involved in meiotic cell cycle->regulation of transcription from RNA polymerase II promoter involved in meiotic cell cycle positive regulation of transcription involved in meiotic cell cycle positive regulation of transcription involved in meiotic cell cycle positive regulation of transcription from RNA polymerase II promoter involved in meiotic cell cycle->positive regulation of transcription involved in meiotic cell cycle positive regulation of transcription involved in meiotic cell cycle->regulation of transcription involved in meiotic cell cycle negative regulation of syncytial blastoderm mitotic cell cycle negative regulation of syncytial blastoderm mitotic cell cycle negative regulation of syncytial blastoderm mitotic cell cycle->regulation of syncytial blastoderm mitotic cell cycle negative regulation of syncytial blastoderm mitotic cell cycle->negative regulation of mitotic cell cycle, embryonic meiotic cell cycle process involved in oocyte maturation meiotic cell cycle process involved in oocyte maturation meiotic cell cycle process involved in oocyte maturation->meiotic cell cycle process cell cycle DNA replication termination cell cycle DNA replication termination cell cycle DNA replication termination->cell cycle process cell cycle DNA replication termination->cell cycle DNA replication
cell_cycle_nodes.to_pickle('targets/cell_cycle_GO.pickle')

Overlap

KEGG_GO_venn(cell_cycle_pathway_genes, cell_cycle_nodes)
<matplotlib_venn._common.VennDiagram at 0x1a9edbf40>

Inflammation

pd.set_option('display.max_rows', 200)
matplotlib_inline.backend_inline.set_matplotlib_formats('svg')

Inflammation Pathways


KEGG

chemokine_pathway_id = 'hsa04062'
TNF_pathway_id = 'hsa04668'
complement_pathway_id = 'hsa04610'
leukocyte_transendothelial_migration_pathway_id = 'hsa04670'
Image(REST.kegg_get(chemokine_pathway_id, 'image').read())
Image(REST.kegg_get(TNF_pathway_id, 'image').read())
Image(REST.kegg_get(complement_pathway_id, 'image').read())
Image(REST.kegg_get(leukocyte_transendothelial_migration_pathway_id, 'image').read())
chemokine_pathway_genes = get_KEGG_pathway_gene_members(chemokine_pathway_id)
TNF_pathway_genes = get_KEGG_pathway_gene_members(TNF_pathway_id)
complement_pathway_genes = get_KEGG_pathway_gene_members(complement_pathway_id)
leukocyte_transendothelial_migration_pathway_genes = get_KEGG_pathway_gene_members(leukocyte_transendothelial_migration_pathway_id)
chemokine_pathway_genes.index = ['Chemokine signaling pathway']*len(chemokine_pathway_genes)
TNF_pathway_genes.index = ['TNF signaling pathway']*len(TNF_pathway_genes)
complement_pathway_genes.index = ['Complement and coagulation cascades']*len(complement_pathway_genes)
leukocyte_transendothelial_migration_pathway_genes.index = ['Leukocyte transendothelial migration']*len(leukocyte_transendothelial_migration_pathway_genes)
inflammation_genes = pd.concat((chemokine_pathway_genes,TNF_pathway_genes,complement_pathway_genes,leukocyte_transendothelial_migration_pathway_genes))
inflammation_genes.to_pickle('targets/inflammation_brite.pickle')

GO

inflammation_subgraph, inflammation_nodes = GO_subgraph_from_query('inflammat')
df = create_GO_by_gene_matrix(inflammation_nodes, attr='gene_name')
df = sort_df_by_hclust_olo(df)

matplotlib_inline.backend_inline.set_matplotlib_formats('png')
ax = plot_gene_membership_in_GO_terms(df, figsize=(6, 10))
draw_graph(inflammation_subgraph)
regulation of acute inflammatory response to non-antigenic stimulus regulation of acute inflammatory response to non-antigenic stimulus regulation of acute inflammatory response regulation of acute inflammatory response regulation of acute inflammatory response to non-antigenic stimulus->regulation of acute inflammatory response regulation of inflammatory response regulation of inflammatory response regulation of acute inflammatory response->regulation of inflammatory response regulation of cytokine production involved in inflammatory response regulation of cytokine production involved in inflammatory response negative regulation of inflammatory response negative regulation of inflammatory response negative regulation of inflammatory response->regulation of inflammatory response negative regulation of neuroinflammatory response negative regulation of neuroinflammatory response negative regulation of neuroinflammatory response->negative regulation of inflammatory response regulation of neuroinflammatory response regulation of neuroinflammatory response negative regulation of neuroinflammatory response->regulation of neuroinflammatory response regulation of neuroinflammatory response->regulation of inflammatory response negative regulation of inflammatory response to wounding negative regulation of inflammatory response to wounding negative regulation of inflammatory response to wounding->negative regulation of inflammatory response regulation of inflammatory response to wounding regulation of inflammatory response to wounding negative regulation of inflammatory response to wounding->regulation of inflammatory response to wounding regulation of inflammatory response to wounding->regulation of inflammatory response regulation of chronic inflammatory response regulation of chronic inflammatory response regulation of chronic inflammatory response->regulation of inflammatory response positive regulation of inflammatory response positive regulation of inflammatory response positive regulation of inflammatory response->regulation of inflammatory response lysosomal enzyme secretion involved in inflammatory response lysosomal enzyme secretion involved in inflammatory response lysosomal enzyme production involved in inflammatory response lysosomal enzyme production involved in inflammatory response lysosomal enzyme secretion involved in inflammatory response->lysosomal enzyme production involved in inflammatory response production of molecular mediator involved in inflammatory response production of molecular mediator involved in inflammatory response lysosomal enzyme production involved in inflammatory response->production of molecular mediator involved in inflammatory response wound healing involved in inflammatory response wound healing involved in inflammatory response inflammatory response to wounding inflammatory response to wounding wound healing involved in inflammatory response->inflammatory response to wounding inflammatory response inflammatory response inflammatory response to wounding->inflammatory response negative regulation of acute inflammatory response to non-antigenic stimulus negative regulation of acute inflammatory response to non-antigenic stimulus negative regulation of acute inflammatory response to non-antigenic stimulus->regulation of acute inflammatory response to non-antigenic stimulus negative regulation of acute inflammatory response negative regulation of acute inflammatory response negative regulation of acute inflammatory response to non-antigenic stimulus->negative regulation of acute inflammatory response negative regulation of acute inflammatory response->regulation of acute inflammatory response negative regulation of acute inflammatory response->negative regulation of inflammatory response negative regulation of macrophage inflammatory protein-1 gamma production negative regulation of macrophage inflammatory protein-1 gamma production regulation of macrophage inflammatory protein-1 gamma production regulation of macrophage inflammatory protein-1 gamma production negative regulation of macrophage inflammatory protein-1 gamma production->regulation of macrophage inflammatory protein-1 gamma production positive regulation of cytokine production involved in inflammatory response positive regulation of cytokine production involved in inflammatory response positive regulation of cytokine production involved in inflammatory response->regulation of cytokine production involved in inflammatory response negative regulation of cytokine production involved in inflammatory response negative regulation of cytokine production involved in inflammatory response negative regulation of cytokine production involved in inflammatory response->regulation of cytokine production involved in inflammatory response prostaglandin production involved in inflammatory response prostaglandin production involved in inflammatory response arachidonic acid metabolite production involved in inflammatory response arachidonic acid metabolite production involved in inflammatory response prostaglandin production involved in inflammatory response->arachidonic acid metabolite production involved in inflammatory response arachidonic acid metabolite production involved in inflammatory response->production of molecular mediator involved in inflammatory response regulation of chronic inflammatory response to non-antigenic stimulus regulation of chronic inflammatory response to non-antigenic stimulus regulation of chronic inflammatory response to non-antigenic stimulus->regulation of chronic inflammatory response positive regulation of respiratory burst involved in inflammatory response positive regulation of respiratory burst involved in inflammatory response positive regulation of respiratory burst involved in inflammatory response->positive regulation of inflammatory response regulation of respiratory burst involved in inflammatory response regulation of respiratory burst involved in inflammatory response positive regulation of respiratory burst involved in inflammatory response->regulation of respiratory burst involved in inflammatory response regulation of respiratory burst involved in inflammatory response->regulation of inflammatory response positive regulation of neuroinflammatory response positive regulation of neuroinflammatory response positive regulation of neuroinflammatory response->regulation of neuroinflammatory response positive regulation of neuroinflammatory response->positive regulation of inflammatory response inflammatory response to antigenic stimulus inflammatory response to antigenic stimulus inflammatory response to antigenic stimulus->inflammatory response serotonin production involved in inflammatory response serotonin production involved in inflammatory response serotonin production involved in inflammatory response->production of molecular mediator involved in inflammatory response production of molecular mediator involved in inflammatory response->inflammatory response negative regulation of chronic inflammatory response negative regulation of chronic inflammatory response negative regulation of chronic inflammatory response->negative regulation of inflammatory response negative regulation of chronic inflammatory response->regulation of chronic inflammatory response acute inflammatory response to antigenic stimulus acute inflammatory response to antigenic stimulus acute inflammatory response to antigenic stimulus->inflammatory response to antigenic stimulus acute inflammatory response acute inflammatory response acute inflammatory response to antigenic stimulus->acute inflammatory response acute inflammatory response->inflammatory response negative regulation of acute inflammatory response to antigenic stimulus negative regulation of acute inflammatory response to antigenic stimulus negative regulation of acute inflammatory response to antigenic stimulus->negative regulation of acute inflammatory response regulation of acute inflammatory response to antigenic stimulus regulation of acute inflammatory response to antigenic stimulus negative regulation of acute inflammatory response to antigenic stimulus->regulation of acute inflammatory response to antigenic stimulus negative regulation of inflammatory response to antigenic stimulus negative regulation of inflammatory response to antigenic stimulus negative regulation of acute inflammatory response to antigenic stimulus->negative regulation of inflammatory response to antigenic stimulus regulation of acute inflammatory response to antigenic stimulus->regulation of acute inflammatory response regulation of inflammatory response to antigenic stimulus regulation of inflammatory response to antigenic stimulus regulation of acute inflammatory response to antigenic stimulus->regulation of inflammatory response to antigenic stimulus negative regulation of inflammatory response to antigenic stimulus->negative regulation of inflammatory response negative regulation of inflammatory response to antigenic stimulus->regulation of inflammatory response to antigenic stimulus leukocyte migration involved in inflammatory response leukocyte migration involved in inflammatory response leukocyte migration involved in inflammatory response->inflammatory response suppression by symbiont of host inflammatory response suppression by symbiont of host inflammatory response modulation by symbiont of host inflammatory response modulation by symbiont of host inflammatory response suppression by symbiont of host inflammatory response->modulation by symbiont of host inflammatory response cytokine production involved in inflammatory response cytokine production involved in inflammatory response cytokine production involved in inflammatory response->production of molecular mediator involved in inflammatory response clearance of damaged tissue involved in inflammatory response wound healing clearance of damaged tissue involved in inflammatory response wound healing clearance of damaged tissue involved in inflammatory response wound healing->wound healing involved in inflammatory response respiratory burst involved in inflammatory response respiratory burst involved in inflammatory response respiratory burst involved in inflammatory response->production of molecular mediator involved in inflammatory response regulation of vascular permeability involved in acute inflammatory response regulation of vascular permeability involved in acute inflammatory response regulation of vascular permeability involved in acute inflammatory response->acute inflammatory response chronic inflammatory response to non-antigenic stimulus chronic inflammatory response to non-antigenic stimulus chronic inflammatory response chronic inflammatory response chronic inflammatory response to non-antigenic stimulus->chronic inflammatory response chronic inflammatory response->inflammatory response macrophage inflammatory protein-1 alpha production macrophage inflammatory protein-1 alpha production inflammatory cell apoptotic process inflammatory cell apoptotic process nitric oxide production involved in inflammatory response nitric oxide production involved in inflammatory response nitric oxide production involved in inflammatory response->production of molecular mediator involved in inflammatory response regulation of connective tissue replacement involved in inflammatory response wound healing regulation of connective tissue replacement involved in inflammatory response wound healing regulation of macrophage inflammatory protein 1 alpha production regulation of macrophage inflammatory protein 1 alpha production acute inflammatory response to non-antigenic stimulus acute inflammatory response to non-antigenic stimulus acute inflammatory response to non-antigenic stimulus->acute inflammatory response negative regulation of respiratory burst involved in inflammatory response negative regulation of respiratory burst involved in inflammatory response negative regulation of respiratory burst involved in inflammatory response->negative regulation of inflammatory response negative regulation of respiratory burst involved in inflammatory response->regulation of respiratory burst involved in inflammatory response positive regulation of chronic inflammatory response to non-antigenic stimulus positive regulation of chronic inflammatory response to non-antigenic stimulus positive regulation of chronic inflammatory response to non-antigenic stimulus->regulation of chronic inflammatory response to non-antigenic stimulus positive regulation of chronic inflammatory response positive regulation of chronic inflammatory response positive regulation of chronic inflammatory response to non-antigenic stimulus->positive regulation of chronic inflammatory response positive regulation of chronic inflammatory response->regulation of chronic inflammatory response positive regulation of chronic inflammatory response->positive regulation of inflammatory response negative regulation of chronic inflammatory response to antigenic stimulus negative regulation of chronic inflammatory response to antigenic stimulus negative regulation of chronic inflammatory response to antigenic stimulus->negative regulation of chronic inflammatory response negative regulation of chronic inflammatory response to antigenic stimulus->negative regulation of inflammatory response to antigenic stimulus regulation of chronic inflammatory response to antigenic stimulus regulation of chronic inflammatory response to antigenic stimulus negative regulation of chronic inflammatory response to antigenic stimulus->regulation of chronic inflammatory response to antigenic stimulus regulation of chronic inflammatory response to antigenic stimulus->regulation of chronic inflammatory response regulation of chronic inflammatory response to antigenic stimulus->regulation of inflammatory response to antigenic stimulus leukotriene production involved in inflammatory response leukotriene production involved in inflammatory response leukotriene production involved in inflammatory response->arachidonic acid metabolite production involved in inflammatory response negative regulation of macrophage inflammatory protein 1 alpha production negative regulation of macrophage inflammatory protein 1 alpha production negative regulation of macrophage inflammatory protein 1 alpha production->regulation of macrophage inflammatory protein 1 alpha production histamine secretion involved in inflammatory response histamine secretion involved in inflammatory response histamine production involved in inflammatory response histamine production involved in inflammatory response histamine secretion involved in inflammatory response->histamine production involved in inflammatory response histamine production involved in inflammatory response->production of molecular mediator involved in inflammatory response vasodilation involved in acute inflammatory response vasodilation involved in acute inflammatory response vasodilation involved in acute inflammatory response->acute inflammatory response activation of plasma proteins involved in acute inflammatory response activation of plasma proteins involved in acute inflammatory response activation of plasma proteins involved in acute inflammatory response->acute inflammatory response regulation of inflammatory response to antigenic stimulus->regulation of inflammatory response positive regulation of chronic inflammatory response to antigenic stimulus positive regulation of chronic inflammatory response to antigenic stimulus positive regulation of chronic inflammatory response to antigenic stimulus->positive regulation of chronic inflammatory response positive regulation of chronic inflammatory response to antigenic stimulus->regulation of chronic inflammatory response to antigenic stimulus positive regulation of inflammatory response to antigenic stimulus positive regulation of inflammatory response to antigenic stimulus positive regulation of chronic inflammatory response to antigenic stimulus->positive regulation of inflammatory response to antigenic stimulus positive regulation of inflammatory response to antigenic stimulus->positive regulation of inflammatory response positive regulation of inflammatory response to antigenic stimulus->regulation of inflammatory response to antigenic stimulus positive regulation by symbiont of host inflammatory response positive regulation by symbiont of host inflammatory response positive regulation by symbiont of host inflammatory response->modulation by symbiont of host inflammatory response positive regulation of connective tissue replacement involved in inflammatory response wound healing positive regulation of connective tissue replacement involved in inflammatory response wound healing positive regulation of connective tissue replacement involved in inflammatory response wound healing->regulation of connective tissue replacement involved in inflammatory response wound healing connective tissue replacement involved in inflammatory response wound healing connective tissue replacement involved in inflammatory response wound healing connective tissue replacement involved in inflammatory response wound healing->wound healing involved in inflammatory response negative regulation of chronic inflammatory response to non-antigenic stimulus negative regulation of chronic inflammatory response to non-antigenic stimulus negative regulation of chronic inflammatory response to non-antigenic stimulus->regulation of chronic inflammatory response to non-antigenic stimulus negative regulation of chronic inflammatory response to non-antigenic stimulus->negative regulation of chronic inflammatory response positive regulation of inflammatory response to wounding positive regulation of inflammatory response to wounding positive regulation of inflammatory response to wounding->regulation of inflammatory response to wounding positive regulation of inflammatory response to wounding->positive regulation of inflammatory response leukocyte chemotaxis involved in inflammatory response leukocyte chemotaxis involved in inflammatory response leukocyte chemotaxis involved in inflammatory response->leukocyte migration involved in inflammatory response platelet activating factor production involved in inflammatory response platelet activating factor production involved in inflammatory response platelet activating factor production involved in inflammatory response->production of molecular mediator involved in inflammatory response positive regulation of acute inflammatory response positive regulation of acute inflammatory response positive regulation of acute inflammatory response->regulation of acute inflammatory response positive regulation of acute inflammatory response->positive regulation of inflammatory response positive regulation of acute inflammatory response to non-antigenic stimulus positive regulation of acute inflammatory response to non-antigenic stimulus positive regulation of acute inflammatory response to non-antigenic stimulus->regulation of acute inflammatory response to non-antigenic stimulus positive regulation of acute inflammatory response to non-antigenic stimulus->positive regulation of acute inflammatory response regulation of leukotriene production involved in inflammatory response regulation of leukotriene production involved in inflammatory response macrophage inflammatory protein-1 gamma production macrophage inflammatory protein-1 gamma production positive regulation of macrophage inflammatory protein 1 alpha production positive regulation of macrophage inflammatory protein 1 alpha production positive regulation of macrophage inflammatory protein 1 alpha production->regulation of macrophage inflammatory protein 1 alpha production neuroinflammatory response neuroinflammatory response neuroinflammatory response->inflammatory response negative regulation of leukotriene production involved in inflammatory response negative regulation of leukotriene production involved in inflammatory response negative regulation of leukotriene production involved in inflammatory response->negative regulation of inflammatory response negative regulation of leukotriene production involved in inflammatory response->regulation of leukotriene production involved in inflammatory response chronic inflammatory response to antigenic stimulus chronic inflammatory response to antigenic stimulus chronic inflammatory response to antigenic stimulus->inflammatory response to antigenic stimulus chronic inflammatory response to antigenic stimulus->chronic inflammatory response positive regulation of macrophage inflammatory protein-1 gamma production positive regulation of macrophage inflammatory protein-1 gamma production positive regulation of macrophage inflammatory protein-1 gamma production->regulation of macrophage inflammatory protein-1 gamma production serotonin secretion involved in inflammatory response serotonin secretion involved in inflammatory response serotonin secretion involved in inflammatory response->serotonin production involved in inflammatory response leukocyte activation involved in inflammatory response leukocyte activation involved in inflammatory response leukocyte activation involved in inflammatory response->inflammatory response positive regulation of acute inflammatory response to antigenic stimulus positive regulation of acute inflammatory response to antigenic stimulus positive regulation of acute inflammatory response to antigenic stimulus->regulation of acute inflammatory response to antigenic stimulus positive regulation of acute inflammatory response to antigenic stimulus->positive regulation of inflammatory response to antigenic stimulus positive regulation of acute inflammatory response to antigenic stimulus->positive regulation of acute inflammatory response negative regulation of connective tissue replacement involved in inflammatory response wound healing negative regulation of connective tissue replacement involved in inflammatory response wound healing negative regulation of connective tissue replacement involved in inflammatory response wound healing->regulation of connective tissue replacement involved in inflammatory response wound healing positive regulation of leukotriene production involved in inflammatory response positive regulation of leukotriene production involved in inflammatory response positive regulation of leukotriene production involved in inflammatory response->positive regulation of inflammatory response positive regulation of leukotriene production involved in inflammatory response->regulation of leukotriene production involved in inflammatory response
inflammation_nodes.to_pickle('targets/inflammation_GO.pickle')

Overlap

matplotlib_inline.backend_inline.set_matplotlib_formats('svg')
KEGG_GO_venn(inflammation_genes, inflammation_nodes)
<matplotlib_venn._common.VennDiagram at 0x1aa368940>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd"> 2022-08-01T19:46:13.515420 image/svg+xml Matplotlib v3.5.2, https://matplotlib.org/

cytokines


KEGG

cytokines_KEGG_BRITE = 'ko04052'
cytokines_brite_genes = get_KEGG_BRITE_entry(cytokines_KEGG_BRITE)
cytokines_brite_genes.to_pickle('targets/cytokines_brite.pickle')

GO

cytokines_subgraph, cytokines_nodes = GO_subgraph_from_query('cytokine')
df = create_GO_by_gene_matrix(cytokines_nodes, attr='gene_name')
df = sort_df_by_hclust_olo(df)

matplotlib_inline.backend_inline.set_matplotlib_formats('png')
ax = plot_gene_membership_in_GO_terms(df, figsize=(6, 10))
draw_graph(cytokines_subgraph)
mitotic cytokinetic process mitotic cytokinetic process mitotic cytokinesis mitotic cytokinesis mitotic cytokinetic process->mitotic cytokinesis cytokinetic process cytokinetic process mitotic cytokinetic process->cytokinetic process cytoskeleton-dependent cytokinesis cytoskeleton-dependent cytokinesis mitotic cytokinesis->cytoskeleton-dependent cytokinesis cytokinesis cytokinesis cytokinetic process->cytokinesis regulation of cytokine production involved in inflammatory response regulation of cytokine production involved in inflammatory response regulation of cytokine production regulation of cytokine production regulation of cytokine production involved in inflammatory response->regulation of cytokine production macrophage cytokine production macrophage cytokine production myeloid leukocyte cytokine production myeloid leukocyte cytokine production macrophage cytokine production->myeloid leukocyte cytokine production cytokine production involved in immune response cytokine production involved in immune response myeloid leukocyte cytokine production->cytokine production involved in immune response mitotic cytokinesis, site selection mitotic cytokinesis, site selection mitotic cytokinesis, site selection->mitotic cytokinetic process cytokinesis, site selection cytokinesis, site selection mitotic cytokinesis, site selection->cytokinesis, site selection cytokinesis, site selection->cytokinetic process positive regulation of cytokine production positive regulation of cytokine production positive regulation of cytokine production->regulation of cytokine production regulation of cytokine production involved in immune response regulation of cytokine production involved in immune response regulation of cytokine production involved in immune response->regulation of cytokine production FtsZ-dependent cytokinesis FtsZ-dependent cytokinesis FtsZ-dependent cytokinesis->cytokinesis regulation of plasmacytoid dendritic cell cytokine production regulation of plasmacytoid dendritic cell cytokine production regulation of dendritic cell cytokine production regulation of dendritic cell cytokine production regulation of plasmacytoid dendritic cell cytokine production->regulation of dendritic cell cytokine production regulation of dendritic cell cytokine production->regulation of cytokine production involved in immune response positive regulation of cytokinesis, actomyosin contractile ring assembly positive regulation of cytokinesis, actomyosin contractile ring assembly regulation of cytokinesis, actomyosin contractile ring assembly regulation of cytokinesis, actomyosin contractile ring assembly positive regulation of cytokinesis, actomyosin contractile ring assembly->regulation of cytokinesis, actomyosin contractile ring assembly positive regulation of cytokinesis positive regulation of cytokinesis positive regulation of cytokinesis, actomyosin contractile ring assembly->positive regulation of cytokinesis regulation of cytokinetic process regulation of cytokinetic process regulation of cytokinesis, actomyosin contractile ring assembly->regulation of cytokinetic process regulation of cytokinesis regulation of cytokinesis positive regulation of cytokinesis->regulation of cytokinesis B cell cytokine production B cell cytokine production B cell cytokine production->cytokine production involved in immune response cytokine production cytokine production cytokine production involved in immune response->cytokine production evasion of host immune response via regulation of host cytokine network evasion of host immune response via regulation of host cytokine network cytokine-mediated signaling pathway cytokine-mediated signaling pathway cellular response to cytokine stimulus cellular response to cytokine stimulus cytokine-mediated signaling pathway->cellular response to cytokine stimulus response to cytokine response to cytokine cellular response to cytokine stimulus->response to cytokine regulation of T cell cytokine production regulation of T cell cytokine production regulation of T cell cytokine production->regulation of cytokine production involved in immune response myosin filament organization involved in cytokinetic actomyosin contractile ring assembly myosin filament organization involved in cytokinetic actomyosin contractile ring assembly regulation of mast cell cytokine production regulation of mast cell cytokine production regulation of mast cell cytokine production->regulation of cytokine production involved in immune response positive regulation of cytokine production involved in inflammatory response positive regulation of cytokine production involved in inflammatory response positive regulation of cytokine production involved in inflammatory response->regulation of cytokine production involved in inflammatory response positive regulation of cytokine production involved in inflammatory response->positive regulation of cytokine production negative regulation of cytokine production involved in inflammatory response negative regulation of cytokine production involved in inflammatory response negative regulation of cytokine production involved in inflammatory response->regulation of cytokine production involved in inflammatory response negative regulation of cytokine production negative regulation of cytokine production negative regulation of cytokine production involved in inflammatory response->negative regulation of cytokine production negative regulation of cytokine production->regulation of cytokine production mast cell cytokine production mast cell cytokine production mast cell cytokine production->myeloid leukocyte cytokine production negative regulation of myeloid dendritic cell cytokine production negative regulation of myeloid dendritic cell cytokine production regulation of myeloid dendritic cell cytokine production regulation of myeloid dendritic cell cytokine production negative regulation of myeloid dendritic cell cytokine production->regulation of myeloid dendritic cell cytokine production negative regulation of dendritic cell cytokine production negative regulation of dendritic cell cytokine production negative regulation of myeloid dendritic cell cytokine production->negative regulation of dendritic cell cytokine production regulation of myeloid dendritic cell cytokine production->regulation of dendritic cell cytokine production negative regulation of dendritic cell cytokine production->regulation of dendritic cell cytokine production negative regulation of cytokine production involved in immune response negative regulation of cytokine production involved in immune response negative regulation of dendritic cell cytokine production->negative regulation of cytokine production involved in immune response positive regulation of plasmacytoid dendritic cell cytokine production positive regulation of plasmacytoid dendritic cell cytokine production positive regulation of plasmacytoid dendritic cell cytokine production->regulation of plasmacytoid dendritic cell cytokine production positive regulation of dendritic cell cytokine production positive regulation of dendritic cell cytokine production positive regulation of plasmacytoid dendritic cell cytokine production->positive regulation of dendritic cell cytokine production positive regulation of dendritic cell cytokine production->regulation of dendritic cell cytokine production positive regulation of cytokine production involved in immune response positive regulation of cytokine production involved in immune response positive regulation of dendritic cell cytokine production->positive regulation of cytokine production involved in immune response positive regulation of response to cytokinesis checkpoint signaling positive regulation of response to cytokinesis checkpoint signaling regulation of response to cytokinesis checkpoint signaling regulation of response to cytokinesis checkpoint signaling positive regulation of response to cytokinesis checkpoint signaling->regulation of response to cytokinesis checkpoint signaling negative regulation of septum digestion after cytokinesis negative regulation of septum digestion after cytokinesis regulation of septum digestion after cytokinesis regulation of septum digestion after cytokinesis negative regulation of septum digestion after cytokinesis->regulation of septum digestion after cytokinesis positive regulation of response to cytokine stimulus positive regulation of response to cytokine stimulus regulation of response to cytokine stimulus regulation of response to cytokine stimulus positive regulation of response to cytokine stimulus->regulation of response to cytokine stimulus negative regulation of cytokine activity negative regulation of cytokine activity regulation of cytokine activity regulation of cytokine activity negative regulation of cytokine activity->regulation of cytokine activity negative regulation of T cell cytokine production negative regulation of T cell cytokine production negative regulation of T cell cytokine production->regulation of T cell cytokine production negative regulation of T cell cytokine production->negative regulation of cytokine production involved in immune response negative regulation of cytokine production involved in immune response->regulation of cytokine production involved in immune response negative regulation of cytokine production involved in immune response->negative regulation of cytokine production cell cycle comprising mitosis without cytokinesis cell cycle comprising mitosis without cytokinesis negative regulation of mast cell cytokine production negative regulation of mast cell cytokine production negative regulation of mast cell cytokine production->regulation of mast cell cytokine production negative regulation of mast cell cytokine production->negative regulation of cytokine production involved in immune response positive regulation of mitotic cytokinesis positive regulation of mitotic cytokinesis positive regulation of mitotic cytokinesis->positive regulation of cytokinesis regulation of mitotic cytokinesis regulation of mitotic cytokinesis positive regulation of mitotic cytokinesis->regulation of mitotic cytokinesis regulation of mitotic cytokinesis->regulation of cytokinesis cytoskeleton-dependent cytokinesis->cytokinesis positive regulation of myeloid dendritic cell cytokine production positive regulation of myeloid dendritic cell cytokine production positive regulation of myeloid dendritic cell cytokine production->regulation of myeloid dendritic cell cytokine production positive regulation of myeloid dendritic cell cytokine production->positive regulation of dendritic cell cytokine production positive regulation of myeloid leukocyte cytokine production involved in immune response positive regulation of myeloid leukocyte cytokine production involved in immune response positive regulation of myeloid dendritic cell cytokine production->positive regulation of myeloid leukocyte cytokine production involved in immune response positive regulation of myeloid leukocyte cytokine production involved in immune response->positive regulation of cytokine production involved in immune response septum digestion after cytokinesis septum digestion after cytokinesis negative regulation of tumor necrosis factor superfamily cytokine production negative regulation of tumor necrosis factor superfamily cytokine production negative regulation of tumor necrosis factor superfamily cytokine production->negative regulation of cytokine production regulation of tumor necrosis factor superfamily cytokine production regulation of tumor necrosis factor superfamily cytokine production negative regulation of tumor necrosis factor superfamily cytokine production->regulation of tumor necrosis factor superfamily cytokine production regulation of tumor necrosis factor superfamily cytokine production->regulation of cytokine production negative regulation of T-helper 2 cell cytokine production negative regulation of T-helper 2 cell cytokine production negative regulation of T-helper 2 cell cytokine production->negative regulation of T cell cytokine production regulation of T-helper 2 cell cytokine production regulation of T-helper 2 cell cytokine production negative regulation of T-helper 2 cell cytokine production->regulation of T-helper 2 cell cytokine production regulation of T-helper 2 cell cytokine production->regulation of T cell cytokine production suppression by virus of host cytokine production suppression by virus of host cytokine production suppression by virus of host cytokine production->negative regulation of cytokine production modulation by virus of host cytokine production modulation by virus of host cytokine production suppression by virus of host cytokine production->modulation by virus of host cytokine production negative regulation of mitotic cytokinesis negative regulation of mitotic cytokinesis negative regulation of mitotic cytokinesis->regulation of mitotic cytokinesis negative regulation of cytokinesis negative regulation of cytokinesis negative regulation of mitotic cytokinesis->negative regulation of cytokinesis negative regulation of cytokinesis->regulation of cytokinesis cytokine production involved in inflammatory response cytokine production involved in inflammatory response cytokine production involved in inflammatory response->cytokine production positive regulation of cytokinesis, site selection positive regulation of cytokinesis, site selection positive regulation of cytokinesis, site selection->positive regulation of cytokinesis regulation of cytokinesis, site selection regulation of cytokinesis, site selection positive regulation of cytokinesis, site selection->regulation of cytokinesis, site selection regulation of cytokinesis, site selection->regulation of cytokinetic process regulation of mitotic cytokinesis, site selection regulation of mitotic cytokinesis, site selection regulation of mitotic cytokinesis, site selection->regulation of cytokinesis, site selection regulation of mitotic cytokinetic process regulation of mitotic cytokinetic process regulation of mitotic cytokinesis, site selection->regulation of mitotic cytokinetic process regulation of mitotic cytokinetic process->regulation of cytokinetic process regulation of mitotic cytokinetic process->regulation of mitotic cytokinesis meiosis I cytokinesis meiosis I cytokinesis meiotic cytokinesis meiotic cytokinesis meiosis I cytokinesis->meiotic cytokinesis meiotic cytokinesis->cytoskeleton-dependent cytokinesis cytokine receptor activity cytokine receptor activity cytokinesis by cell plate formation cytokinesis by cell plate formation cytokinesis by cell plate formation->cytokinesis protein localization to cell division site after cytokinesis protein localization to cell division site after cytokinesis negative regulation of macrophage cytokine production negative regulation of macrophage cytokine production negative regulation of macrophage cytokine production->negative regulation of cytokine production involved in immune response regulation of macrophage cytokine production regulation of macrophage cytokine production negative regulation of macrophage cytokine production->regulation of macrophage cytokine production regulation of macrophage cytokine production->regulation of cytokine production involved in immune response positive regulation of cytokine production involved in immune response->positive regulation of cytokine production positive regulation of cytokine production involved in immune response->regulation of cytokine production involved in immune response mitotic cytokinesis checkpoint signaling mitotic cytokinesis checkpoint signaling positive regulation of septum digestion after cytokinesis positive regulation of septum digestion after cytokinesis positive regulation of septum digestion after cytokinesis->regulation of septum digestion after cytokinesis negative regulation of plasmacytoid dendritic cell cytokine production negative regulation of plasmacytoid dendritic cell cytokine production negative regulation of plasmacytoid dendritic cell cytokine production->regulation of plasmacytoid dendritic cell cytokine production negative regulation of plasmacytoid dendritic cell cytokine production->negative regulation of dendritic cell cytokine production negative regulation of mitotic cytokinetic process negative regulation of mitotic cytokinetic process negative regulation of mitotic cytokinetic process->negative regulation of mitotic cytokinesis negative regulation of mitotic cytokinetic process->regulation of mitotic cytokinetic process regulation of FtsZ-dependent cytokinesis regulation of FtsZ-dependent cytokinesis regulation of FtsZ-dependent cytokinesis->regulation of cytokinesis negative regulation of cytokinesis, actomyosin contractile ring assembly negative regulation of cytokinesis, actomyosin contractile ring assembly negative regulation of cytokinesis, actomyosin contractile ring assembly->regulation of cytokinesis, actomyosin contractile ring assembly negative regulation of cytokinesis, actomyosin contractile ring assembly->negative regulation of cytokinesis negative regulation of B cell cytokine production negative regulation of B cell cytokine production negative regulation of B cell cytokine production->negative regulation of cytokine production involved in immune response regulation of B cell cytokine production regulation of B cell cytokine production negative regulation of B cell cytokine production->regulation of B cell cytokine production regulation of B cell cytokine production->regulation of cytokine production involved in immune response regulation of protein localization to cell division site involved in cytokinesis regulation of protein localization to cell division site involved in cytokinesis regulation of protein localization to cell division site involved in cytokinesis->cytokinesis protein localization to cell division site involved in cytokinesis, actomyosin contractile ring assembly protein localization to cell division site involved in cytokinesis, actomyosin contractile ring assembly positive regulation of tumor necrosis factor superfamily cytokine production positive regulation of tumor necrosis factor superfamily cytokine production positive regulation of tumor necrosis factor superfamily cytokine production->positive regulation of cytokine production positive regulation of tumor necrosis factor superfamily cytokine production->regulation of tumor necrosis factor superfamily cytokine production membrane addition at site of mitotic cytokinesis membrane addition at site of mitotic cytokinesis membrane addition at site of mitotic cytokinesis->mitotic cytokinetic process membrane addition at site of cytokinesis membrane addition at site of cytokinesis membrane addition at site of mitotic cytokinesis->membrane addition at site of cytokinesis membrane addition at site of cytokinesis->cytokinetic process cytokine precursor processing cytokine precursor processing cytokine precursor processing->cytokine production T cell cytokine production T cell cytokine production T cell cytokine production->cytokine production involved in immune response positive regulation of mitotic cytokinesis, site selection positive regulation of mitotic cytokinesis, site selection positive regulation of mitotic cytokinesis, site selection->positive regulation of cytokinesis, site selection positive regulation of mitotic cytokinesis, site selection->regulation of mitotic cytokinesis, site selection positive regulation of mitotic cytokinetic process positive regulation of mitotic cytokinetic process positive regulation of mitotic cytokinesis, site selection->positive regulation of mitotic cytokinetic process positive regulation of mitotic cytokinetic process->positive regulation of mitotic cytokinesis positive regulation of mitotic cytokinetic process->regulation of mitotic cytokinetic process suppression by virus of host cytokine activity suppression by virus of host cytokine activity negative regulation of cytokinesis, site selection negative regulation of cytokinesis, site selection negative regulation of cytokinesis, site selection->negative regulation of cytokinesis negative regulation of cytokinesis, site selection->regulation of cytokinesis, site selection CD4-positive, alpha-beta T cell cytokine production CD4-positive, alpha-beta T cell cytokine production CD4-positive, alpha-beta T cell cytokine production->T cell cytokine production regulation of protein localization to cell division site involved in cell separation after cytokinesis regulation of protein localization to cell division site involved in cell separation after cytokinesis regulation of protein localization to cell division site involved in cell separation after cytokinesis->septum digestion after cytokinesis regulation of cytokine-mediated signaling pathway regulation of cytokine-mediated signaling pathway regulation of cytokine-mediated signaling pathway->regulation of response to cytokine stimulus positive regulation of FtsZ-dependent cytokinesis positive regulation of FtsZ-dependent cytokinesis positive regulation of FtsZ-dependent cytokinesis->positive regulation of cytokinesis positive regulation of FtsZ-dependent cytokinesis->regulation of FtsZ-dependent cytokinesis assembly of actomyosin apparatus involved in mitotic cytokinesis assembly of actomyosin apparatus involved in mitotic cytokinesis assembly of actomyosin apparatus involved in mitotic cytokinesis->mitotic cytokinetic process assembly of actomyosin apparatus involved in cytokinesis assembly of actomyosin apparatus involved in cytokinesis assembly of actomyosin apparatus involved in mitotic cytokinesis->assembly of actomyosin apparatus involved in cytokinesis assembly of actomyosin apparatus involved in cytokinesis->cytokinetic process assembly of actomyosin apparatus involved in cytokinesis->cytoskeleton-dependent cytokinesis regulation of natural killer cell cytokine production regulation of natural killer cell cytokine production regulation of natural killer cell cytokine production->regulation of cytokine production involved in immune response tumor necrosis factor superfamily cytokine production tumor necrosis factor superfamily cytokine production tumor necrosis factor superfamily cytokine production->cytokine production positive regulation of mast cell cytokine production positive regulation of mast cell cytokine production positive regulation of mast cell cytokine production->regulation of mast cell cytokine production positive regulation of mast cell cytokine production->positive regulation of myeloid leukocyte cytokine production involved in immune response T-helper 2 cell cytokine production T-helper 2 cell cytokine production T-helper 2 cell cytokine production->CD4-positive, alpha-beta T cell cytokine production positive regulation of macrophage cytokine production positive regulation of macrophage cytokine production positive regulation of macrophage cytokine production->positive regulation of myeloid leukocyte cytokine production involved in immune response positive regulation of macrophage cytokine production->regulation of macrophage cytokine production Cdv-dependent cytokinesis Cdv-dependent cytokinesis Cdv-dependent cytokinesis->cytokinesis guard mother cell cytokinesis guard mother cell cytokinesis guard mother cell cytokinesis->cytokinesis by cell plate formation positive regulation of cytokine activity positive regulation of cytokine activity positive regulation of cytokine activity->regulation of cytokine activity positive regulation of T-helper 2 cell cytokine production positive regulation of T-helper 2 cell cytokine production positive regulation of T-helper 2 cell cytokine production->regulation of T-helper 2 cell cytokine production positive regulation of T cell cytokine production positive regulation of T cell cytokine production positive regulation of T-helper 2 cell cytokine production->positive regulation of T cell cytokine production positive regulation of T cell cytokine production->regulation of T cell cytokine production positive regulation of T cell cytokine production->positive regulation of cytokine production involved in immune response male meiosis cytokinesis male meiosis cytokinesis male meiosis cytokinesis->meiotic cytokinesis regulation of actin filament organization involved in cytokinetic actomyosin contractile ring assembly regulation of actin filament organization involved in cytokinetic actomyosin contractile ring assembly response to cytokinesis checkpoint signaling response to cytokinesis checkpoint signaling meiosis II cytokinesis meiosis II cytokinesis meiosis II cytokinesis->meiotic cytokinesis negative regulation of natural killer cell cytokine production negative regulation of natural killer cell cytokine production negative regulation of natural killer cell cytokine production->negative regulation of cytokine production involved in immune response negative regulation of natural killer cell cytokine production->regulation of natural killer cell cytokine production signal transduction involved in cytokinesis checkpoint signal transduction involved in cytokinesis checkpoint cytokine binding cytokine binding positive regulation of T-helper 1 cell cytokine production positive regulation of T-helper 1 cell cytokine production positive regulation of T-helper 1 cell cytokine production->positive regulation of T cell cytokine production regulation of T-helper 1 cell cytokine production regulation of T-helper 1 cell cytokine production positive regulation of T-helper 1 cell cytokine production->regulation of T-helper 1 cell cytokine production regulation of T-helper 1 cell cytokine production->regulation of T cell cytokine production suppression by symbiont of host cytokine production suppression by symbiont of host cytokine production syncytium formation by mitosis without cytokinesis syncytium formation by mitosis without cytokinesis dendritic cell cytokine production dendritic cell cytokine production dendritic cell cytokine production->cytokine production involved in immune response myeloid dendritic cell cytokine production myeloid dendritic cell cytokine production myeloid dendritic cell cytokine production->myeloid leukocyte cytokine production myeloid dendritic cell cytokine production->dendritic cell cytokine production induction by virus of host cytokine production induction by virus of host cytokine production induction by virus of host cytokine production->positive regulation of cytokine production induction by virus of host cytokine production->modulation by virus of host cytokine production negative regulation of response to cytokine stimulus negative regulation of response to cytokine stimulus negative regulation of response to cytokine stimulus->regulation of response to cytokine stimulus positive regulation of B cell cytokine production positive regulation of B cell cytokine production positive regulation of B cell cytokine production->positive regulation of cytokine production involved in immune response positive regulation of B cell cytokine production->regulation of B cell cytokine production natural killer cell cytokine production natural killer cell cytokine production natural killer cell cytokine production->cytokine production involved in immune response protein localization to cell division site involved in cell separation after cytokinesis protein localization to cell division site involved in cell separation after cytokinesis protein localization to cell division site involved in cell separation after cytokinesis->septum digestion after cytokinesis negative regulation of FtsZ-dependent cytokinesis negative regulation of FtsZ-dependent cytokinesis negative regulation of FtsZ-dependent cytokinesis->negative regulation of cytokinesis negative regulation of FtsZ-dependent cytokinesis->regulation of FtsZ-dependent cytokinesis negative regulation of T-helper 1 cell cytokine production negative regulation of T-helper 1 cell cytokine production negative regulation of T-helper 1 cell cytokine production->negative regulation of T cell cytokine production negative regulation of T-helper 1 cell cytokine production->regulation of T-helper 1 cell cytokine production negative regulation of cytokine-mediated signaling pathway negative regulation of cytokine-mediated signaling pathway negative regulation of cytokine-mediated signaling pathway->regulation of cytokine-mediated signaling pathway negative regulation of cytokine-mediated signaling pathway->negative regulation of response to cytokine stimulus T-helper 1 cell cytokine production T-helper 1 cell cytokine production T-helper 1 cell cytokine production->CD4-positive, alpha-beta T cell cytokine production cytokine receptor binding cytokine receptor binding positive regulation of cytokine-mediated signaling pathway positive regulation of cytokine-mediated signaling pathway positive regulation of cytokine-mediated signaling pathway->positive regulation of response to cytokine stimulus positive regulation of cytokine-mediated signaling pathway->regulation of cytokine-mediated signaling pathway positive regulation of natural killer cell cytokine production positive regulation of natural killer cell cytokine production positive regulation of natural killer cell cytokine production->positive regulation of cytokine production involved in immune response positive regulation of natural killer cell cytokine production->regulation of natural killer cell cytokine production plasmacytoid dendritic cell cytokine production plasmacytoid dendritic cell cytokine production plasmacytoid dendritic cell cytokine production->dendritic cell cytokine production cytokine activity cytokine activity zygote asymmetric cytokinesis in embryo sac zygote asymmetric cytokinesis in embryo sac zygote asymmetric cytokinesis in embryo sac->mitotic cytokinesis
cytokines_nodes.to_pickle('targets/cytokines_GO.pickle')

Overlap

matplotlib_inline.backend_inline.set_matplotlib_formats('svg')
KEGG_GO_venn(cytokines_brite_genes, cytokines_nodes)
<matplotlib_venn._common.VennDiagram at 0x1aaae7040>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd"> 2022-08-01T19:46:43.065532 image/svg+xml Matplotlib v3.5.2, https://matplotlib.org/

cGAS-STING


KEGG

cGAS_STING_pathway_id = 'hsa04623'
Image(REST.kegg_get(cGAS_STING_pathway_id, 'image').read())
cGAS_STING_pathway_genes = get_KEGG_pathway_gene_members(cGAS_STING_pathway_id)
cGAS_STING_pathway_genes.to_pickle('targets/cGAS_STING_kegg.pickle')

GO

cGAS_STING_subgraph, cGAS_STING_nodes = GO_subgraph_from_query('activation of innate immune response')
draw_graph(cGAS_STING_subgraph)
activation of innate immune response activation of innate immune response
cGAS_STING_nodes.to_pickle('targets/cGAS_STING_GO.pickle')

Overlap

KEGG_GO_venn(cGAS_STING_pathway_genes, cGAS_STING_nodes)
<matplotlib_venn._common.VennDiagram at 0x1aaa85340>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd"> 2022-08-01T19:46:46.451775 image/svg+xml Matplotlib v3.5.2, https://matplotlib.org/

senescence programs


KEGG

senescence_pathway = 'hsa04218'
Image(REST.kegg_get(senescence_pathway, 'image').read())
senescence_pathway_genes = get_KEGG_pathway_gene_members(senescence_pathway)
senescence_pathway_genes.to_pickle('targets/senescence_kegg.pickle')

GO

senescence_subgraph, senescence_nodes = GO_subgraph_from_query('senescence')
df = create_GO_by_gene_matrix(senescence_nodes, attr='gene_name')
df = sort_df_by_hclust_olo(df)

matplotlib_inline.backend_inline.set_matplotlib_formats('svg')
ax = plot_gene_membership_in_GO_terms(df, figsize=(6, 10))
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd"> 2022-08-01T19:46:50.753292 image/svg+xml Matplotlib v3.5.2, https://matplotlib.org/
draw_graph(senescence_subgraph)
plant organ senescence plant organ senescence cellular senescence cellular senescence regulation of replicative senescence regulation of replicative senescence regulation of cellular senescence regulation of cellular senescence negative regulation of leaf senescence negative regulation of leaf senescence regulation of leaf senescence regulation of leaf senescence negative regulation of leaf senescence->regulation of leaf senescence replicative senescence replicative senescence senescence-associated vacuole senescence-associated vacuole oncogene-induced cell senescence oncogene-induced cell senescence oncogene-induced cell senescence->cellular senescence senescence-associated heterochromatin focus senescence-associated heterochromatin focus stress-induced premature senescence stress-induced premature senescence stress-induced premature senescence->cellular senescence negative regulation of replicative senescence negative regulation of replicative senescence negative regulation of replicative senescence->regulation of replicative senescence negative regulation of cellular senescence negative regulation of cellular senescence negative regulation of cellular senescence->regulation of cellular senescence oxidative stress-induced premature senescence oxidative stress-induced premature senescence oxidative stress-induced premature senescence->stress-induced premature senescence floral organ senescence floral organ senescence floral organ senescence->plant organ senescence reproductive senescence reproductive senescence positive regulation of leaf senescence positive regulation of leaf senescence positive regulation of leaf senescence->regulation of leaf senescence positive regulation of cellular senescence positive regulation of cellular senescence positive regulation of cellular senescence->regulation of cellular senescence positive regulation of replicative senescence positive regulation of replicative senescence positive regulation of replicative senescence->regulation of replicative senescence leaf senescence leaf senescence leaf senescence->plant organ senescence
senescence_nodes.to_pickle('targets/senescence_GO.pickle')

Overlap

KEGG_GO_venn(senescence_pathway_genes, senescence_nodes)
<matplotlib_venn._common.VennDiagram at 0x1a9ed3400>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd"> 2022-08-01T19:46:51.104733 image/svg+xml Matplotlib v3.5.2, https://matplotlib.org/

inflammasome activation


KEGG

inflammasome_pathway = 'hsa04621'
Image(REST.kegg_get(inflammasome_pathway, 'image').read())
inflammasome_pathway_genes = get_KEGG_pathway_gene_members(inflammasome_pathway)
inflammasome_pathway_genes.to_pickle('targets/inflammasome_kegg.pickle')

GO

inflammasome_subgraph, inflammasome_nodes = GO_subgraph_from_query('inflammasome')
df = create_GO_by_gene_matrix(inflammasome_nodes, attr='gene_name')
df = sort_df_by_hclust_olo(df)

# matplotlib_inline.backend_inline.set_matplotlib_formats('svg')
ax = plot_gene_membership_in_GO_terms(df, figsize=(6, 10))
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd"> 2022-08-01T19:46:55.037351 image/svg+xml Matplotlib v3.5.2, https://matplotlib.org/
draw_graph(inflammasome_subgraph)
IPAF inflammasome complex IPAF inflammasome complex inflammasome complex inflammasome complex IPAF inflammasome complex->inflammasome complex NLRP1 inflammasome complex NLRP1 inflammasome complex NLRP1 inflammasome complex->inflammasome complex positive regulation of NLRP3 inflammasome complex assembly positive regulation of NLRP3 inflammasome complex assembly regulation of NLRP3 inflammasome complex assembly regulation of NLRP3 inflammasome complex assembly positive regulation of NLRP3 inflammasome complex assembly->regulation of NLRP3 inflammasome complex assembly NLRP6 inflammasome complex assembly NLRP6 inflammasome complex assembly inflammasome complex assembly inflammasome complex assembly NLRP6 inflammasome complex assembly->inflammasome complex assembly negative regulation of NLRP3 inflammasome complex assembly negative regulation of NLRP3 inflammasome complex assembly negative regulation of NLRP3 inflammasome complex assembly->regulation of NLRP3 inflammasome complex assembly AIM2 inflammasome complex AIM2 inflammasome complex AIM2 inflammasome complex->inflammasome complex CARD8 inflammasome complex CARD8 inflammasome complex CARD8 inflammasome complex->inflammasome complex NLRP1 inflammasome complex assembly NLRP1 inflammasome complex assembly NLRP1 inflammasome complex assembly->inflammasome complex assembly NLRP3 inflammasome complex NLRP3 inflammasome complex NLRP3 inflammasome complex->inflammasome complex NLRP3 inflammasome complex assembly NLRP3 inflammasome complex assembly NLRP3 inflammasome complex assembly->inflammasome complex assembly CARD8 inflammasome complex assembly CARD8 inflammasome complex assembly CARD8 inflammasome complex assembly->inflammasome complex assembly NLRP6 inflammasome complex NLRP6 inflammasome complex NLRP6 inflammasome complex->inflammasome complex
inflammasome_nodes.to_pickle('targets/inflammasome_GO.pickle')

Overlap

KEGG_GO_venn(inflammasome_pathway_genes, inflammasome_nodes)
<matplotlib_venn._common.VennDiagram at 0x199e98a00>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd"> 2022-08-01T19:46:55.303127 image/svg+xml Matplotlib v3.5.2, https://matplotlib.org/

Metabolic Defects

Glycolysis


KEGG

glycolysis_pathway_id = 'hsa00010'
# glycolysis_brite_id = 'ko03051'
Image(REST.kegg_get(glycolysis_pathway_id, 'image').read())
glycolysis_pathway_genes = get_KEGG_pathway_gene_members(glycolysis_pathway_id)
# proteasome_brite_genes = proteasome_brite_genes.loc['Eukaryotic proteasome']
# proteasome_brite_genes['in_KEGG_pathway'] = proteasome_brite_genes.ENSG.isin(proteasome_pathway_genes.ENSG).astype(int)
glycolysis_pathway_genes.to_pickle('targets/glycolysis_kegg.pickle')

GO

glycolysis_subgraph, glycolysis_nodes = GO_subgraph_from_query('glycolysis')
df = create_GO_by_gene_matrix(glycolysis_nodes, attr='gene_name')
df = sort_df_by_hclust_olo(df)
ax = plot_gene_membership_in_GO_terms(df, figsize=(6, 10))
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd"> 2022-08-01T19:46:58.301281 image/svg+xml Matplotlib v3.5.2, https://matplotlib.org/
draw_graph(glycolysis_subgraph)
canonical glycolysis canonical glycolysis glycolysis from storage polysaccharide through glucose-1-phosphate glycolysis from storage polysaccharide through glucose-1-phosphate sulphoglycolysis sulphoglycolysis
glycolysis_nodes.to_pickle('targets/glycolysis_GO.pickle')

Overlap

KEGG_GO_venn(glycolysis_pathway_genes, glycolysis_nodes)
<matplotlib_venn._common.VennDiagram at 0x19a013910>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd"> 2022-08-01T19:46:58.509224 image/svg+xml Matplotlib v3.5.2, https://matplotlib.org/

TCA Cycle


KEGG

tca_pathway_id = 'hsa00020'
# tca_brite_id = 'ko03051'
Image(REST.kegg_get(tca_pathway_id, 'image').read())
tca_pathway_genes = get_KEGG_pathway_gene_members(tca_pathway_id)
# proteasome_brite_genes = proteasome_brite_genes.loc['Eukaryotic proteasome']
# proteasome_brite_genes['in_KEGG_pathway'] = proteasome_brite_genes.ENSG.isin(proteasome_pathway_genes.ENSG).astype(int)
tca_pathway_genes.to_pickle('targets/tca_kegg.pickle')

GO

tca_subgraph, tca_nodes = GO_subgraph_from_query('tricarboxylic acid cycle')
df = create_GO_by_gene_matrix(tca_nodes, attr='gene_name')
df = sort_df_by_hclust_olo(df)
ax = plot_gene_membership_in_GO_terms(df, figsize=(6, 10))
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd"> 2022-08-01T19:47:01.609924 image/svg+xml Matplotlib v3.5.2, https://matplotlib.org/
draw_graph(tca_subgraph)
cytosolic tricarboxylic acid cycle enzyme complex cytosolic tricarboxylic acid cycle enzyme complex tricarboxylic acid cycle enzyme complex tricarboxylic acid cycle enzyme complex cytosolic tricarboxylic acid cycle enzyme complex->tricarboxylic acid cycle enzyme complex mitochondrial tricarboxylic acid cycle enzyme complex mitochondrial tricarboxylic acid cycle enzyme complex mitochondrial tricarboxylic acid cycle enzyme complex->tricarboxylic acid cycle enzyme complex reductive tricarboxylic acid cycle reductive tricarboxylic acid cycle tricarboxylic acid cycle tricarboxylic acid cycle reductive tricarboxylic acid cycle->tricarboxylic acid cycle
tca_nodes.to_pickle('targets/tca_GO.pickle')

Overlap

KEGG_GO_venn(tca_pathway_genes, tca_nodes)
<matplotlib_venn._common.VennDiagram at 0x1a9631f10>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd"> 2022-08-01T19:47:01.868275 image/svg+xml Matplotlib v3.5.2, https://matplotlib.org/

electron transport chain


KEGG

ETC_pathway = 'hsa00190'
Image(REST.kegg_get(ETC_pathway, 'image').read())
ETC_pathway_genes = get_KEGG_pathway_gene_members(ETC_pathway)
ETC_pathway_genes.to_pickle('targets/ETC_kegg.pickle')

GO

ETC_subgraph, ETC_nodes = GO_subgraph_from_query('electron transport chain')
df = create_GO_by_gene_matrix(ETC_nodes, attr='gene_name')
df = sort_df_by_hclust_olo(df)
ax = plot_gene_membership_in_GO_terms(df, figsize=(6, 10))
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd"> 2022-08-01T19:47:06.028776 image/svg+xml Matplotlib v3.5.2, https://matplotlib.org/
draw_graph(ETC_subgraph)
respiratory electron transport chain respiratory electron transport chain electron transport chain electron transport chain respiratory electron transport chain->electron transport chain nitrate reductase activity involved in anaerobic electron transport chain nitrate reductase activity involved in anaerobic electron transport chain P450-containing electron transport chain P450-containing electron transport chain P450-containing electron transport chain->electron transport chain anaerobic electron transport chain anaerobic electron transport chain anaerobic electron transport chain->respiratory electron transport chain aerobic electron transport chain aerobic electron transport chain aerobic electron transport chain->respiratory electron transport chain photosynthetic electron transport chain photosynthetic electron transport chain photosynthetic electron transport chain->electron transport chain
ETC_nodes.to_pickle('targets/ETC_GO.pickle')

Overlap

KEGG_GO_venn(ETC_pathway_genes, ETC_nodes)
<matplotlib_venn._common.VennDiagram at 0x1aa018970>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd"> 2022-08-01T19:47:06.349479 image/svg+xml Matplotlib v3.5.2, https://matplotlib.org/

mitochondrial biogenesis


KEGG

pd.set_option('display.max_rows', 200)
mitochondrial_biogenesis_brite_id = 'ko03029'
mitochondrial_biogenesis_brite_genes = get_KEGG_BRITE_entry(mitochondrial_biogenesis_brite_id)
mitochondrial_biogenesis_brite_genes = mitochondrial_biogenesis_brite_genes.loc[['Mitochondrial DNA transcription, translation, and replication factors','Mitochondrial quality control factors']]
# mitochondrial_biogenesis_brite.loc['Mitochondrial DNA transcription, translation, and replication factors']
mitochondrial_biogenesis_brite_genes.to_pickle('targets/mitochondrial_biogenesis_brite.pickle')

GO

mitochondrial_biogenesis_subgraph, mitochondrial_biogenesis_nodes = GO_subgraph_from_query('mitochondrial fission')
draw_graph(mitochondrial_biogenesis_subgraph)
negative regulation of mitochondrial fission negative regulation of mitochondrial fission regulation of mitochondrial fission regulation of mitochondrial fission negative regulation of mitochondrial fission->regulation of mitochondrial fission positive regulation of mitochondrial fission positive regulation of mitochondrial fission positive regulation of mitochondrial fission->regulation of mitochondrial fission establishment of protein localization to mitochondrial membrane involved in mitochondrial fission establishment of protein localization to mitochondrial membrane involved in mitochondrial fission mitochondrial fission mitochondrial fission establishment of protein localization to mitochondrial membrane involved in mitochondrial fission->mitochondrial fission dynamin family protein polymerization involved in mitochondrial fission dynamin family protein polymerization involved in mitochondrial fission
mitochondrial_biogenesis_nodes.to_pickle('targets/mitochondrial_biogenesis_GO.pickle')

Overlap

KEGG_GO_venn(mitochondrial_biogenesis_brite_genes, mitochondrial_biogenesis_nodes)
<matplotlib_venn._common.VennDiagram at 0x1aa214a90>
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oxidative stress


GO

oxidative_stress_subgraph, oxidative_stress_nodes = GO_subgraph_from_query('oxidative stress')
draw_graph(oxidative_stress_subgraph)
regulation of mRNA stability involved in response to oxidative stress regulation of mRNA stability involved in response to oxidative stress response to oxidative stress response to oxidative stress regulation of mRNA stability involved in response to oxidative stress->response to oxidative stress regulation of oxidative stress-induced intrinsic apoptotic signaling pathway regulation of oxidative stress-induced intrinsic apoptotic signaling pathway regulation of oxidative stress-induced cell death regulation of oxidative stress-induced cell death regulation of oxidative stress-induced intrinsic apoptotic signaling pathway->regulation of oxidative stress-induced cell death regulation of cellular response to oxidative stress regulation of cellular response to oxidative stress regulation of oxidative stress-induced cell death->regulation of cellular response to oxidative stress intrinsic apoptotic signaling pathway in response to oxidative stress intrinsic apoptotic signaling pathway in response to oxidative stress cell death in response to oxidative stress cell death in response to oxidative stress intrinsic apoptotic signaling pathway in response to oxidative stress->cell death in response to oxidative stress cellular response to oxidative stress cellular response to oxidative stress cell death in response to oxidative stress->cellular response to oxidative stress regulation of transcription from RNA polymerase II promoter in response to oxidative stress regulation of transcription from RNA polymerase II promoter in response to oxidative stress regulation of transcription from RNA polymerase II promoter in response to oxidative stress->cellular response to oxidative stress cellular response to oxidative stress->response to oxidative stress positive regulation of oxidative stress-induced cell death positive regulation of oxidative stress-induced cell death positive regulation of oxidative stress-induced cell death->regulation of oxidative stress-induced cell death positive regulation of cellular response to oxidative stress positive regulation of cellular response to oxidative stress positive regulation of cellular response to oxidative stress->regulation of cellular response to oxidative stress positive regulation of response to oxidative stress positive regulation of response to oxidative stress positive regulation of cellular response to oxidative stress->positive regulation of response to oxidative stress regulation of response to oxidative stress regulation of response to oxidative stress regulation of cellular response to oxidative stress->regulation of response to oxidative stress positive regulation of response to oxidative stress->regulation of response to oxidative stress detection of oxidative stress detection of oxidative stress detection of oxidative stress->response to oxidative stress positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway->regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway->positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway positive regulation of oxidative stress-induced neuron death positive regulation of oxidative stress-induced neuron death positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway->positive regulation of oxidative stress-induced neuron death regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway->regulation of oxidative stress-induced intrinsic apoptotic signaling pathway regulation of oxidative stress-induced neuron death regulation of oxidative stress-induced neuron death regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway->regulation of oxidative stress-induced neuron death positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway->regulation of oxidative stress-induced intrinsic apoptotic signaling pathway positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway->positive regulation of oxidative stress-induced cell death positive regulation of oxidative stress-induced neuron death->positive regulation of oxidative stress-induced cell death positive regulation of oxidative stress-induced neuron death->regulation of oxidative stress-induced neuron death positive regulation of translation in response to oxidative stress positive regulation of translation in response to oxidative stress positive regulation of translation in response to oxidative stress->cellular response to oxidative stress negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway->regulation of oxidative stress-induced intrinsic apoptotic signaling pathway negative regulation of oxidative stress-induced cell death negative regulation of oxidative stress-induced cell death negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway->negative regulation of oxidative stress-induced cell death negative regulation of oxidative stress-induced cell death->regulation of oxidative stress-induced cell death neuron death in response to oxidative stress neuron death in response to oxidative stress neuron death in response to oxidative stress->cell death in response to oxidative stress negative regulation of response to oxidative stress negative regulation of response to oxidative stress negative regulation of response to oxidative stress->regulation of response to oxidative stress negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway->regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway->negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway negative regulation of oxidative stress-induced neuron death negative regulation of oxidative stress-induced neuron death negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway->negative regulation of oxidative stress-induced neuron death negative regulation of oxidative stress-induced neuron death->negative regulation of oxidative stress-induced cell death negative regulation of oxidative stress-induced neuron death->regulation of oxidative stress-induced neuron death regulation of translation in response to oxidative stress regulation of translation in response to oxidative stress regulation of translation in response to oxidative stress->cellular response to oxidative stress negative regulation of cellular response to oxidative stress negative regulation of cellular response to oxidative stress negative regulation of cellular response to oxidative stress->regulation of cellular response to oxidative stress negative regulation of cellular response to oxidative stress->negative regulation of response to oxidative stress regulation of oxidative stress-induced neuron death->regulation of oxidative stress-induced cell death negative regulation of translation in response to oxidative stress negative regulation of translation in response to oxidative stress negative regulation of translation in response to oxidative stress->regulation of translation in response to oxidative stress neuron intrinsic apoptotic signaling pathway in response to oxidative stress neuron intrinsic apoptotic signaling pathway in response to oxidative stress neuron intrinsic apoptotic signaling pathway in response to oxidative stress->intrinsic apoptotic signaling pathway in response to oxidative stress neuron intrinsic apoptotic signaling pathway in response to oxidative stress->neuron death in response to oxidative stress positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress->regulation of transcription from RNA polymerase II promoter in response to oxidative stress oxidative stress-induced premature senescence oxidative stress-induced premature senescence oxidative stress-induced premature senescence->cellular response to oxidative stress negative regulation of transcription from RNA polymerase II promoter in response to oxidative stress negative regulation of transcription from RNA polymerase II promoter in response to oxidative stress negative regulation of transcription from RNA polymerase II promoter in response to oxidative stress->regulation of transcription from RNA polymerase II promoter in response to oxidative stress response to photooxidative stress response to photooxidative stress response to photooxidative stress->response to oxidative stress
oxidative_stress_nodes.to_pickle('targets/oxidative_stress_GO.pickle')